diff --git a/packages/backend/src/azuredevops.ts b/packages/backend/src/azuredevops.ts
index 1f9c089b..de587935 100644
--- a/packages/backend/src/azuredevops.ts
+++ b/packages/backend/src/azuredevops.ts
@@ -1,6 +1,6 @@
 import { AzureDevOpsConnectionConfig } from "@sourcebot/schemas/v3/azuredevops.type";
 import { createLogger } from "@sourcebot/logger";
-import { getTokenFromConfig, measure, fetchWithRetry } from "./utils.js";
+import { measure, fetchWithRetry } from "./utils.js";
 import micromatch from "micromatch";
 import { PrismaClient } from "@sourcebot/db";
 import { BackendException, BackendError } from "@sourcebot/error";
@@ -8,6 +8,7 @@ import { processPromiseResults, throwIfAnyFailed } from "./connectionUtils.js";
 import * as Sentry from "@sentry/node";
 import * as azdev from "azure-devops-node-api";
 import { GitRepository } from "azure-devops-node-api/interfaces/GitInterfaces.js";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 
 const logger = createLogger('azuredevops');
 const AZUREDEVOPS_CLOUD_HOSTNAME = "dev.azure.com";
@@ -34,7 +35,7 @@ export const getAzureDevOpsReposFromConfig = async (
     const baseUrl = config.url || `https://${AZUREDEVOPS_CLOUD_HOSTNAME}`;
 
     const token = config.token ?
-        await getTokenFromConfig(config.token, orgId, db, logger) :
+        await getTokenFromConfig(config.token, orgId, db) :
         undefined;
 
     if (!token) {
diff --git a/packages/backend/src/bitbucket.ts b/packages/backend/src/bitbucket.ts
index ae4d6b40..75adc311 100644
--- a/packages/backend/src/bitbucket.ts
+++ b/packages/backend/src/bitbucket.ts
@@ -4,7 +4,7 @@ import { BitbucketConnectionConfig } from "@sourcebot/schemas/v3/bitbucket.type"
 import type { ClientOptions, ClientPathsWithMethod } from "openapi-fetch";
 import { createLogger } from "@sourcebot/logger";
 import { PrismaClient } from "@sourcebot/db";
-import { getTokenFromConfig, measure, fetchWithRetry } from "./utils.js";
+import { measure, fetchWithRetry } from "./utils.js";
 import * as Sentry from "@sentry/node";
 import {
     SchemaRepository as CloudRepository,
@@ -12,6 +12,7 @@ import {
 import { SchemaRestRepository as ServerRepository } from "@coderabbitai/bitbucket/server/openapi";
 import { processPromiseResults } from "./connectionUtils.js";
 import { throwIfAnyFailed } from "./connectionUtils.js";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 
 const logger = createLogger('bitbucket');
 const BITBUCKET_CLOUD_GIT = 'https://bitbucket.org';
@@ -59,7 +60,7 @@ type ServerPaginatedResponse<T> = {
 
 export const getBitbucketReposFromConfig = async (config: BitbucketConnectionConfig, orgId: number, db: PrismaClient) => {
     const token = config.token ?
-        await getTokenFromConfig(config.token, orgId, db, logger) :
+        await getTokenFromConfig(config.token, orgId, db) :
         undefined;
 
     if (config.deploymentType === 'server' && !config.url) {
diff --git a/packages/backend/src/ee/githubAppManager.ts b/packages/backend/src/ee/githubAppManager.ts
index 2518c27b..ad4aa247 100644
--- a/packages/backend/src/ee/githubAppManager.ts
+++ b/packages/backend/src/ee/githubAppManager.ts
@@ -1,8 +1,7 @@
-import { GithubAppConfig, SourcebotConfig } from "@sourcebot/schemas/v3/index.type";
 import { loadConfig } from "@sourcebot/shared";
 import { env } from "../env.js";
 import { createLogger } from "@sourcebot/logger";
-import { getTokenFromConfig } from "../utils.js";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 import { PrismaClient } from "@sourcebot/db";
 import { App } from "@octokit/app";
 import { GitHubAppConfig } from "@sourcebot/schemas/v3/index.type";
@@ -54,7 +53,7 @@ export class GithubAppManager {
             return;
         }
 
-        const githubApps = config.apps.filter(app => app.type === 'githubApp') as GithubAppConfig[];
+        const githubApps = config.apps.filter(app => app.type === 'githubApp') as GitHubAppConfig[];
         logger.info(`Found ${githubApps.length} GitHub apps in config`);
 
         for (const app of githubApps) {
@@ -63,7 +62,7 @@ export class GithubAppManager {
             // @todo: we should move SINGLE_TENANT_ORG_ID to shared package or just remove the need to pass this in 
             // when resolving tokens
             const SINGLE_TENANT_ORG_ID = 1;
-            const privateKey = await getTokenFromConfig(app.privateKey, SINGLE_TENANT_ORG_ID, this.db!);
+            const privateKey = await getTokenFromConfig(app.privateKey, SINGLE_TENANT_ORG_ID, this.db);
 
             const octokitApp = new App({
                 appId: Number(app.id),
diff --git a/packages/backend/src/gitea.ts b/packages/backend/src/gitea.ts
index 5dca28d3..ab3eee3f 100644
--- a/packages/backend/src/gitea.ts
+++ b/packages/backend/src/gitea.ts
@@ -1,6 +1,6 @@
 import { Api, giteaApi, HttpResponse, Repository as GiteaRepository } from 'gitea-js';
 import { GiteaConnectionConfig } from '@sourcebot/schemas/v3/gitea.type';
-import { getTokenFromConfig, measure } from './utils.js';
+import { measure } from './utils.js';
 import fetch from 'cross-fetch';
 import { createLogger } from '@sourcebot/logger';
 import micromatch from 'micromatch';
@@ -8,6 +8,7 @@ import { PrismaClient } from '@sourcebot/db';
 import { processPromiseResults, throwIfAnyFailed } from './connectionUtils.js';
 import * as Sentry from "@sentry/node";
 import { env } from './env.js';
+import { getTokenFromConfig } from "@sourcebot/crypto";
 
 const logger = createLogger('gitea');
 const GITEA_CLOUD_HOSTNAME = "gitea.com";
@@ -18,7 +19,7 @@ export const getGiteaReposFromConfig = async (config: GiteaConnectionConfig, org
         GITEA_CLOUD_HOSTNAME;
 
     const token = config.token ?
-        await getTokenFromConfig(config.token, orgId, db, logger) :
+        await getTokenFromConfig(config.token, orgId, db) :
         hostname === GITEA_CLOUD_HOSTNAME ?
         env.FALLBACK_GITEA_CLOUD_TOKEN :
         undefined;
diff --git a/packages/backend/src/github.ts b/packages/backend/src/github.ts
index 464bb7b1..550d259d 100644
--- a/packages/backend/src/github.ts
+++ b/packages/backend/src/github.ts
@@ -8,7 +8,8 @@ import micromatch from "micromatch";
 import { processPromiseResults, throwIfAnyFailed } from "./connectionUtils.js";
 import { GithubAppManager } from "./ee/githubAppManager.js";
 import { env } from "./env.js";
-import { fetchWithRetry, getTokenFromConfig, measure } from "./utils.js";
+import { fetchWithRetry, measure } from "./utils.js";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 
 export const GITHUB_CLOUD_HOSTNAME = "github.com";
 const logger = createLogger('github');
@@ -97,7 +98,7 @@ export const getGitHubReposFromConfig = async (config: GithubConnectionConfig, o
         GITHUB_CLOUD_HOSTNAME;
 
     const token = config.token ?
-        await getTokenFromConfig(config.token, orgId, db, logger) :
+        await getTokenFromConfig(config.token, orgId, db) :
         hostname === GITHUB_CLOUD_HOSTNAME ?
             env.FALLBACK_GITHUB_CLOUD_TOKEN :
             undefined;
diff --git a/packages/backend/src/gitlab.ts b/packages/backend/src/gitlab.ts
index de52e64d..e4954b34 100644
--- a/packages/backend/src/gitlab.ts
+++ b/packages/backend/src/gitlab.ts
@@ -2,11 +2,12 @@ import { Gitlab, ProjectSchema } from "@gitbeaker/rest";
 import micromatch from "micromatch";
 import { createLogger } from "@sourcebot/logger";
 import { GitlabConnectionConfig } from "@sourcebot/schemas/v3/gitlab.type"
-import { getTokenFromConfig, measure, fetchWithRetry } from "./utils.js";
+import { measure, fetchWithRetry } from "./utils.js";
 import { PrismaClient } from "@sourcebot/db";
 import { processPromiseResults, throwIfAnyFailed } from "./connectionUtils.js";
 import * as Sentry from "@sentry/node";
 import { env } from "./env.js";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 
 const logger = createLogger('gitlab');
 export const GITLAB_CLOUD_HOSTNAME = "gitlab.com";
@@ -17,7 +18,7 @@ export const getGitLabReposFromConfig = async (config: GitlabConnectionConfig, o
         GITLAB_CLOUD_HOSTNAME;
 
     const token = config.token ?
-        await getTokenFromConfig(config.token, orgId, db, logger) :
+        await getTokenFromConfig(config.token, orgId, db) :
         hostname === GITLAB_CLOUD_HOSTNAME ?
         env.FALLBACK_GITLAB_CLOUD_TOKEN :
         undefined;
diff --git a/packages/backend/src/utils.ts b/packages/backend/src/utils.ts
index 8a1d0cc6..4bb18549 100644
--- a/packages/backend/src/utils.ts
+++ b/packages/backend/src/utils.ts
@@ -2,8 +2,7 @@ import { Logger } from "winston";
 import { RepoAuthCredentials, RepoWithConnections } from "./types.js";
 import path from 'path';
 import { PrismaClient, Repo } from "@sourcebot/db";
-import { getTokenFromConfig as getTokenFromConfigBase } from "@sourcebot/crypto";
-import { BackendException, BackendError } from "@sourcebot/error";
+import { getTokenFromConfig } from "@sourcebot/crypto";
 import * as Sentry from "@sentry/node";
 import { GithubConnectionConfig, GitlabConnectionConfig, GiteaConnectionConfig, BitbucketConnectionConfig, AzureDevOpsConnectionConfig } from '@sourcebot/schemas/v3/connection.type';
 import { GithubAppManager } from "./ee/githubAppManager.js";
@@ -24,22 +23,6 @@ export const marshalBool = (value?: boolean) => {
     return !!value ? '1' : '0';
 }
 
-export const getTokenFromConfig = async (token: any, orgId: number, db: PrismaClient, logger?: Logger) => {
-    try {
-        return await getTokenFromConfigBase(token, orgId, db);
-    } catch (error: unknown) {
-        if (error instanceof Error) {
-            const e = new BackendException(BackendError.CONNECTION_SYNC_SECRET_DNE, {
-                message: error.message,
-            });
-            Sentry.captureException(e);
-            logger?.error(error.message);
-            throw e;
-        }
-        throw error;
-    }
-};
-
 export const resolvePathRelativeToConfig = (localPath: string, configPath: string) => {
     let absolutePath = localPath;
     if (!path.isAbsolute(absolutePath)) {
@@ -156,7 +139,7 @@ export const getAuthCredentialsForRepo = async (repo: RepoWithConnections, db: P
         if (connection.connectionType === 'github') {
             const config = connection.config as unknown as GithubConnectionConfig;
             if (config.token) {
-                const token = await getTokenFromConfig(config.token, connection.orgId, db, logger);
+                const token = await getTokenFromConfig(config.token, connection.orgId, db);
                 return {
                     hostUrl: config.url,
                     token,
@@ -171,7 +154,7 @@ export const getAuthCredentialsForRepo = async (repo: RepoWithConnections, db: P
         } else if (connection.connectionType === 'gitlab') {
             const config = connection.config as unknown as GitlabConnectionConfig;
             if (config.token) {
-                const token = await getTokenFromConfig(config.token, connection.orgId, db, logger);
+                const token = await getTokenFromConfig(config.token, connection.orgId, db);
                 return {
                     hostUrl: config.url,
                     token,
@@ -187,7 +170,7 @@ export const getAuthCredentialsForRepo = async (repo: RepoWithConnections, db: P
         } else if (connection.connectionType === 'gitea') {
             const config = connection.config as unknown as GiteaConnectionConfig;
             if (config.token) {
-                const token = await getTokenFromConfig(config.token, connection.orgId, db, logger);
+                const token = await getTokenFromConfig(config.token, connection.orgId, db);
                 return {
                     hostUrl: config.url,
                     token,
@@ -202,7 +185,7 @@ export const getAuthCredentialsForRepo = async (repo: RepoWithConnections, db: P
         } else if (connection.connectionType === 'bitbucket') {
             const config = connection.config as unknown as BitbucketConnectionConfig;
             if (config.token) {
-                const token = await getTokenFromConfig(config.token, connection.orgId, db, logger);
+                const token = await getTokenFromConfig(config.token, connection.orgId, db);
                 const username = config.user ?? 'x-token-auth';
                 return {
                     hostUrl: config.url,
@@ -219,7 +202,7 @@ export const getAuthCredentialsForRepo = async (repo: RepoWithConnections, db: P
         } else if (connection.connectionType === 'azuredevops') {
             const config = connection.config as unknown as AzureDevOpsConnectionConfig;
             if (config.token) {
-                const token = await getTokenFromConfig(config.token, connection.orgId, db, logger);
+                const token = await getTokenFromConfig(config.token, connection.orgId, db);
 
                 // For ADO server, multiple auth schemes may be supported. If the ADO deployment supports NTLM, the git clone will default
                 // to this over basic auth. As a result, we cannot embed the token in the clone URL and must force basic auth by passing in the token
diff --git a/packages/web/src/actions.ts b/packages/web/src/actions.ts
index 6cacac68..7c3a472a 100644
--- a/packages/web/src/actions.ts
+++ b/packages/web/src/actions.ts
@@ -10,7 +10,7 @@ import { prisma } from "@/prisma";
 import { render } from "@react-email/components";
 import * as Sentry from '@sentry/nextjs';
 import { encrypt, generateApiKey, getTokenFromConfig, hashSecret } from "@sourcebot/crypto";
-import { ApiKey, Org, OrgRole, Prisma, RepoIndexingJobStatus, RepoIndexingJobType, StripeSubscriptionStatus } from "@sourcebot/db";
+import { ApiKey, ConnectionSyncJobStatus, Org, OrgRole, Prisma, RepoIndexingJobStatus, RepoIndexingJobType, StripeSubscriptionStatus } from "@sourcebot/db";
 import { createLogger } from "@sourcebot/logger";
 import { GiteaConnectionConfig } from "@sourcebot/schemas/v3/gitea.type";
 import { GithubConnectionConfig } from "@sourcebot/schemas/v3/github.type";
@@ -30,7 +30,7 @@ import JoinRequestSubmittedEmail from "./emails/joinRequestSubmittedEmail";
 import { AGENTIC_SEARCH_TUTORIAL_DISMISSED_COOKIE_NAME, MOBILE_UNSUPPORTED_SPLASH_SCREEN_DISMISSED_COOKIE_NAME, SINGLE_TENANT_ORG_DOMAIN, SOURCEBOT_GUEST_USER_ID, SOURCEBOT_SUPPORT_EMAIL } from "./lib/constants";
 import { orgDomainSchema, orgNameSchema, repositoryQuerySchema } from "./lib/schemas";
 import { ApiKeyPayload, TenancyMode } from "./lib/types";
-import { withOptionalAuthV2 } from "./withAuthV2";
+import { withAuthV2, withOptionalAuthV2 } from "./withAuthV2";
 
 const logger = createLogger('web-actions');
 const auditService = getAuditService();
@@ -593,6 +593,7 @@ export const getReposStats = async () => sew(() =>
             prisma.repo.count({
                 where: {
                     orgId: org.id,
+                    indexedAt: null,
                     jobs: {
                         some: {
                             type: RepoIndexingJobType.INDEX,
@@ -604,7 +605,6 @@ export const getReposStats = async () => sew(() =>
                             }
                         },
                     },
-                    indexedAt: null,
                 }
             }),
             prisma.repo.count({
@@ -625,6 +625,42 @@ export const getReposStats = async () => sew(() =>
     })
 )
 
+export const getConnectionStats = async () => sew(() =>
+    withAuthV2(async ({ org, prisma }) => {
+        const [
+            numberOfConnections,
+            numberOfConnectionsWithFirstTimeSyncJobsInProgress,
+        ] = await Promise.all([
+            prisma.connection.count({
+                where: {
+                    orgId: org.id,
+                }
+            }),
+            prisma.connection.count({
+                where: {
+                    orgId: org.id,
+                    syncedAt: null,
+                    syncJobs: {
+                        some: {
+                            status: {
+                                in: [
+                                    ConnectionSyncJobStatus.PENDING,
+                                    ConnectionSyncJobStatus.IN_PROGRESS,
+                                ]
+                            }
+                        }
+                    }
+                }
+            })
+        ]);
+
+        return {
+            numberOfConnections,
+            numberOfConnectionsWithFirstTimeSyncJobsInProgress,
+        };
+    })
+);
+
 export const getRepoInfoByName = async (repoName: string) => sew(() =>
     withOptionalAuthV2(async ({ org, prisma }) => {
         // @note: repo names are represented by their remote url
diff --git a/packages/web/src/app/[domain]/components/navigationMenu/index.tsx b/packages/web/src/app/[domain]/components/navigationMenu/index.tsx
index 54842731..f350fe92 100644
--- a/packages/web/src/app/[domain]/components/navigationMenu/index.tsx
+++ b/packages/web/src/app/[domain]/components/navigationMenu/index.tsx
@@ -1,4 +1,4 @@
-import { getRepos, getReposStats } from "@/actions";
+import { getConnectionStats, getRepos, getReposStats } from "@/actions";
 import { SourcebotLogo } from "@/app/components/sourcebotLogo";
 import { auth } from "@/auth";
 import { Button } from "@/components/ui/button";
@@ -39,6 +39,11 @@ export const NavigationMenu = async ({
         throw new ServiceErrorException(repoStats);
     }
 
+    const connectionStats = isAuthenticated ? await getConnectionStats() : null;
+    if (isServiceError(connectionStats)) {
+        throw new ServiceErrorException(connectionStats);
+    }
+
     const sampleRepos = await getRepos({
         where: {
             jobs: {
@@ -93,7 +98,12 @@ export const NavigationMenu = async ({
                         <NavigationItems
                             domain={domain}
                             numberOfRepos={numberOfRepos}
-                            numberOfReposWithFirstTimeIndexingJobsInProgress={numberOfReposWithFirstTimeIndexingJobsInProgress}
+                            isReposButtonNotificationDotVisible={numberOfReposWithFirstTimeIndexingJobsInProgress > 0}
+                            isSettingsButtonNotificationDotVisible={
+                                connectionStats ?
+                                    connectionStats.numberOfConnectionsWithFirstTimeSyncJobsInProgress > 0 :
+                                    false
+                            }
                             isAuthenticated={isAuthenticated}
                         />
                     </NavigationMenuBase>
diff --git a/packages/web/src/app/[domain]/components/navigationMenu/navigationItems.tsx b/packages/web/src/app/[domain]/components/navigationMenu/navigationItems.tsx
index 52db3315..b5a31483 100644
--- a/packages/web/src/app/[domain]/components/navigationMenu/navigationItems.tsx
+++ b/packages/web/src/app/[domain]/components/navigationMenu/navigationItems.tsx
@@ -3,20 +3,23 @@
 import { NavigationMenuItem, NavigationMenuLink, NavigationMenuList, navigationMenuTriggerStyle } from "@/components/ui/navigation-menu";
 import { Badge } from "@/components/ui/badge";
 import { cn, getShortenedNumberDisplayString } from "@/lib/utils";
-import { SearchIcon, MessageCircleIcon, BookMarkedIcon, SettingsIcon, CircleIcon } from "lucide-react";
+import { SearchIcon, MessageCircleIcon, BookMarkedIcon, SettingsIcon } from "lucide-react";
 import { usePathname } from "next/navigation";
+import { NotificationDot } from "../notificationDot";
 
 interface NavigationItemsProps {
     domain: string;
     numberOfRepos: number;
-    numberOfReposWithFirstTimeIndexingJobsInProgress: number;
+    isReposButtonNotificationDotVisible: boolean;
+    isSettingsButtonNotificationDotVisible: boolean;
     isAuthenticated: boolean;
 }
 
 export const NavigationItems = ({
     domain,
     numberOfRepos,
-    numberOfReposWithFirstTimeIndexingJobsInProgress,
+    isReposButtonNotificationDotVisible,
+    isSettingsButtonNotificationDotVisible,
     isAuthenticated,
 }: NavigationItemsProps) => {
     const pathname = usePathname();
@@ -59,9 +62,7 @@ export const NavigationItems = ({
                     <span className="mr-2">Repositories</span>
                     <Badge variant="secondary" className="px-1.5 relative">
                         {getShortenedNumberDisplayString(numberOfRepos)}
-                        {numberOfReposWithFirstTimeIndexingJobsInProgress > 0 && (
-                            <CircleIcon className="absolute -right-0.5 -top-0.5 h-2 w-2 text-green-600" fill="currentColor" />
-                        )}
+                        {isReposButtonNotificationDotVisible && <NotificationDot className="absolute -right-0.5 -top-0.5" />}
                     </Badge>
                 </NavigationMenuLink>
                 {isActive(`/${domain}/repos`) && <ActiveIndicator />}
@@ -74,6 +75,7 @@ export const NavigationItems = ({
                     >
                         <SettingsIcon className="w-4 h-4 mr-1" />
                         Settings
+                        {isSettingsButtonNotificationDotVisible && <NotificationDot className="absolute -right-0.5 -top-0.5" />}
                     </NavigationMenuLink>
                     {isActive(`/${domain}/settings`) && <ActiveIndicator />}
                 </NavigationMenuItem>
@@ -86,4 +88,4 @@ const ActiveIndicator = () => {
     return (
         <div className="absolute -bottom-2 left-0 right-0 h-0.5 bg-foreground" />
     );
-};
\ No newline at end of file
+};
diff --git a/packages/web/src/app/[domain]/components/notificationDot.tsx b/packages/web/src/app/[domain]/components/notificationDot.tsx
new file mode 100644
index 00000000..79624705
--- /dev/null
+++ b/packages/web/src/app/[domain]/components/notificationDot.tsx
@@ -0,0 +1,9 @@
+import { cn } from "@/lib/utils"
+
+interface NotificationDotProps {
+    className?: string
+}
+
+export const NotificationDot = ({ className }: NotificationDotProps) => {
+    return <div className={cn("w-2 h-2 rounded-full bg-green-600", className)} />
+}
\ No newline at end of file
diff --git a/packages/web/src/app/[domain]/repos/components/reposTable.tsx b/packages/web/src/app/[domain]/repos/components/reposTable.tsx
index 2030c4c9..730a2585 100644
--- a/packages/web/src/app/[domain]/repos/components/reposTable.tsx
+++ b/packages/web/src/app/[domain]/repos/components/reposTable.tsx
@@ -37,6 +37,7 @@ import { useRouter } from "next/navigation"
 import { useToast } from "@/components/hooks/use-toast";
 import { DisplayDate } from "../../components/DisplayDate"
 import { Tooltip, TooltipContent, TooltipTrigger } from "@/components/ui/tooltip"
+import { NotificationDot } from "../../components/notificationDot"
 
 // @see: https://v0.app/chat/repo-indexing-status-uhjdDim8OUS
 
@@ -53,6 +54,7 @@ export type Repo = {
     imageUrl: string | null
     indexedCommitHash: string | null
     latestJobStatus: "PENDING" | "IN_PROGRESS" | "COMPLETED" | "FAILED" | null
+    isFirstTimeIndex: boolean
 }
 
 const statusBadgeVariants = cva("", {
@@ -111,14 +113,32 @@ export const columns: ColumnDef<Repo>[] = [
                             {repo.displayName?.charAt(0) ?? repo.name.charAt(0)}
                         </div>
                     )}
-                    <Link href={getBrowsePath({
-                        repoName: repo.name,
-                        path: '/',
-                        pathType: 'tree',
-                        domain: SINGLE_TENANT_ORG_DOMAIN,
-                    })} className="font-medium hover:underline">
+
+                    {/* Link to the details page (instead of browse) when the repo is indexing
+                        as the code will not be available yet */}
+                    <Link
+                        href={repo.isFirstTimeIndex ? `/${SINGLE_TENANT_ORG_DOMAIN}/repos/${repo.id}` : getBrowsePath({
+                            repoName: repo.name,
+                            path: '/',
+                            pathType: 'tree',
+                            domain: SINGLE_TENANT_ORG_DOMAIN,
+                        })}
+                        className="font-medium hover:underline"
+                    >
                         {repo.displayName || repo.name}
                     </Link>
+                    {repo.isFirstTimeIndex && (
+                        <Tooltip>
+                            <TooltipTrigger asChild>
+                                <span>
+                                    <NotificationDot className="ml-1.5" />
+                                </span>
+                            </TooltipTrigger>
+                            <TooltipContent>
+                                <span>This is the first time Sourcebot is indexing this repository. It may take a few minutes to complete.</span>
+                            </TooltipContent>
+                        </Tooltip>
+                    )}
                 </div>
             )
         },
@@ -150,7 +170,7 @@ export const columns: ColumnDef<Repo>[] = [
             }
 
             return (
-                <DisplayDate date={indexedAt} className="ml-3"/>
+                <DisplayDate date={indexedAt} className="ml-3" />
             )
         }
     },
@@ -177,11 +197,11 @@ export const columns: ColumnDef<Repo>[] = [
 
             const HashComponent = commitUrl ? (
                 <Link
-                href={commitUrl}
-                className="font-mono text-sm text-link hover:underline"
-            >
-                {smallHash}
-            </Link>
+                    href={commitUrl}
+                    className="font-mono text-sm text-link hover:underline"
+                >
+                    {smallHash}
+                </Link>
             ) : (
                 <span className="font-mono text-sm text-muted-foreground">
                     {smallHash}
@@ -337,7 +357,7 @@ export const ReposTable = ({ data }: { data: Repo[] }) => {
                             <TableRow key={headerGroup.id}>
                                 {headerGroup.headers.map((header) => {
                                     return (
-                                        <TableHead 
+                                        <TableHead
                                             key={header.id}
                                             style={{ width: `${header.getSize()}px` }}
                                         >
@@ -353,7 +373,7 @@ export const ReposTable = ({ data }: { data: Repo[] }) => {
                             table.getRowModel().rows.map((row) => (
                                 <TableRow key={row.id} data-state={row.getIsSelected() && "selected"}>
                                     {row.getVisibleCells().map((cell) => (
-                                        <TableCell 
+                                        <TableCell
                                             key={cell.id}
                                             style={{ width: `${cell.column.getSize()}px` }}
                                         >
diff --git a/packages/web/src/app/[domain]/repos/page.tsx b/packages/web/src/app/[domain]/repos/page.tsx
index 31830e46..79c4497b 100644
--- a/packages/web/src/app/[domain]/repos/page.tsx
+++ b/packages/web/src/app/[domain]/repos/page.tsx
@@ -3,14 +3,31 @@ import { ServiceErrorException } from "@/lib/serviceError";
 import { isServiceError } from "@/lib/utils";
 import { withOptionalAuthV2 } from "@/withAuthV2";
 import { ReposTable } from "./components/reposTable";
+import { RepoIndexingJobStatus } from "@sourcebot/db";
 
 export default async function ReposPage() {
 
-    const repos = await getReposWithLatestJob();
-    if (isServiceError(repos)) {
-        throw new ServiceErrorException(repos);
+    const _repos = await getReposWithLatestJob();
+    if (isServiceError(_repos)) {
+        throw new ServiceErrorException(_repos);
     }
 
+    const repos = _repos
+        .map((repo) => ({
+            ...repo,
+            latestJobStatus: repo.jobs.length > 0 ? repo.jobs[0].status : null,
+            isFirstTimeIndex: repo.indexedAt === null && repo.jobs.filter((job) => job.status === RepoIndexingJobStatus.PENDING || job.status === RepoIndexingJobStatus.IN_PROGRESS).length > 0,
+        }))
+        .sort((a, b) => {
+            if (a.isFirstTimeIndex && !b.isFirstTimeIndex) {
+                return -1;
+            }
+            if (!a.isFirstTimeIndex && b.isFirstTimeIndex) {
+                return 1;
+            }
+            return a.name.localeCompare(b.name);
+        });
+
     return (
         <>
             <div className="mb-6">
@@ -27,7 +44,8 @@ export default async function ReposPage() {
                 createdAt: repo.createdAt,
                 webUrl: repo.webUrl,
                 imageUrl: repo.imageUrl,
-                latestJobStatus: repo.jobs.length > 0 ? repo.jobs[0].status : null,
+                latestJobStatus: repo.latestJobStatus,
+                isFirstTimeIndex: repo.isFirstTimeIndex,
                 codeHostType: repo.external_codeHostType,
                 indexedCommitHash: repo.indexedCommitHash,
             }))} />
diff --git a/packages/web/src/app/[domain]/settings/components/sidebar-nav.tsx b/packages/web/src/app/[domain]/settings/components/sidebar-nav.tsx
index 393773ec..78b5a7cc 100644
--- a/packages/web/src/app/[domain]/settings/components/sidebar-nav.tsx
+++ b/packages/web/src/app/[domain]/settings/components/sidebar-nav.tsx
@@ -1,15 +1,17 @@
 "use client"
 
-import React from "react"
+import { buttonVariants } from "@/components/ui/button"
+import { NotificationDot } from "@/app/[domain]/components/notificationDot"
+import { cn } from "@/lib/utils"
 import Link from "next/link"
 import { usePathname } from "next/navigation"
-import { cn } from "@/lib/utils"
-import { buttonVariants } from "@/components/ui/button"
+import React from "react"
 
 export type SidebarNavItem = {
     href: string
     hrefRegex?: string
     title: React.ReactNode
+    isNotificationDotVisible?: boolean
 }
 
 interface SidebarNavProps extends React.HTMLAttributes<HTMLElement> {
@@ -43,6 +45,7 @@ export function SidebarNav({ className, items, ...props }: SidebarNavProps) {
                         )}
                     >
                         {item.title}
+                        {item.isNotificationDotVisible && <NotificationDot className="ml-1.5" />}
                     </Link>
                 )
             })}
diff --git a/packages/web/src/app/[domain]/settings/connections/components/connectionsTable.tsx b/packages/web/src/app/[domain]/settings/connections/components/connectionsTable.tsx
index 299a012c..cae2d9c4 100644
--- a/packages/web/src/app/[domain]/settings/connections/components/connectionsTable.tsx
+++ b/packages/web/src/app/[domain]/settings/connections/components/connectionsTable.tsx
@@ -1,12 +1,14 @@
 "use client"
 
 import { DisplayDate } from "@/app/[domain]/components/DisplayDate"
+import { NotificationDot } from "@/app/[domain]/components/notificationDot"
 import { useToast } from "@/components/hooks/use-toast"
 import { Badge } from "@/components/ui/badge"
 import { Button } from "@/components/ui/button"
 import { Input } from "@/components/ui/input"
 import { Select, SelectContent, SelectItem, SelectTrigger, SelectValue } from "@/components/ui/select"
 import { Table, TableBody, TableCell, TableHead, TableHeader, TableRow } from "@/components/ui/table"
+import { Tooltip, TooltipContent, TooltipTrigger } from "@/components/ui/tooltip"
 import { SINGLE_TENANT_ORG_DOMAIN } from "@/lib/constants"
 import { CodeHostType, getCodeHostIcon } from "@/lib/utils"
 import {
@@ -35,6 +37,7 @@ export type Connection = {
     syncedAt: Date | null
     codeHostType: CodeHostType
     latestJobStatus: "PENDING" | "IN_PROGRESS" | "COMPLETED" | "FAILED" | null
+    isFirstTimeSync: boolean
 }
 
 const statusBadgeVariants = cva("", {
@@ -91,6 +94,18 @@ export const columns: ColumnDef<Connection>[] = [
                     <Link href={`/${SINGLE_TENANT_ORG_DOMAIN}/settings/connections/${connection.id}`} className="font-medium hover:underline">
                         {connection.name}
                     </Link>
+                    {connection.isFirstTimeSync && (
+                        <Tooltip>
+                            <TooltipTrigger asChild>
+                                <span>
+                                    <NotificationDot className="ml-1.5" />
+                                </span>
+                            </TooltipTrigger>
+                            <TooltipContent>
+                                <span>This is the first time Sourcebot is syncing this connection. It may take a few minutes to complete.</span>
+                            </TooltipContent>
+                        </Tooltip>
+                    )}
                 </div>
             )
         },
diff --git a/packages/web/src/app/[domain]/settings/connections/page.tsx b/packages/web/src/app/[domain]/settings/connections/page.tsx
index 30d803a5..0701a312 100644
--- a/packages/web/src/app/[domain]/settings/connections/page.tsx
+++ b/packages/web/src/app/[domain]/settings/connections/page.tsx
@@ -4,15 +4,33 @@ import { CodeHostType, isServiceError } from "@/lib/utils";
 import { withAuthV2 } from "@/withAuthV2";
 import Link from "next/link";
 import { ConnectionsTable } from "./components/connectionsTable";
+import { ConnectionSyncJobStatus } from "@prisma/client";
 
 const DOCS_URL = "https://docs.sourcebot.dev/docs/connections/overview";
 
 export default async function ConnectionsPage() {
-    const connections = await getConnectionsWithLatestJob();
-    if (isServiceError(connections)) {
-        throw new ServiceErrorException(connections);
+    const _connections = await getConnectionsWithLatestJob();
+    if (isServiceError(_connections)) {
+        throw new ServiceErrorException(_connections);
     }
 
+    // Sort connections so that first time syncs are at the top.
+    const connections = _connections
+        .map((connection) => ({
+            ...connection,
+            isFirstTimeSync: connection.syncedAt === null && connection.syncJobs.filter((job) => job.status === ConnectionSyncJobStatus.PENDING || job.status === ConnectionSyncJobStatus.IN_PROGRESS).length > 0,
+            latestJobStatus: connection.syncJobs.length > 0 ? connection.syncJobs[0].status : null,
+        }))
+        .sort((a, b) => {
+            if (a.isFirstTimeSync && !b.isFirstTimeSync) {
+                return -1;
+            }
+            if (!a.isFirstTimeSync && b.isFirstTimeSync) {
+                return 1;
+            }
+            return a.name.localeCompare(b.name);
+        });
+
     return (
         <div className="flex flex-col gap-6">
             <div>
@@ -24,7 +42,8 @@ export default async function ConnectionsPage() {
                 name: connection.name,
                 codeHostType: connection.connectionType as CodeHostType,
                 syncedAt: connection.syncedAt,
-                latestJobStatus: connection.syncJobs.length > 0 ? connection.syncJobs[0].status : null,
+                latestJobStatus: connection.latestJobStatus,
+                isFirstTimeSync: connection.isFirstTimeSync,
             }))} />
         </div>
     )
@@ -34,16 +53,22 @@ const getConnectionsWithLatestJob = async () => sew(() =>
     withAuthV2(async ({ prisma }) => {
         const connections = await prisma.connection.findMany({
             include: {
+                _count: {
+                    select: {
+                        syncJobs: true,
+                    }
+                },
                 syncJobs: {
                     orderBy: {
                         createdAt: 'desc'
                     },
                     take: 1
-                }
+                },
             },
             orderBy: {
                 name: 'asc'
-            }
+            },
         });
+
         return connections;
     }));
\ No newline at end of file
diff --git a/packages/web/src/app/[domain]/settings/layout.tsx b/packages/web/src/app/[domain]/settings/layout.tsx
index fcb11f66..a68c54f1 100644
--- a/packages/web/src/app/[domain]/settings/layout.tsx
+++ b/packages/web/src/app/[domain]/settings/layout.tsx
@@ -6,7 +6,7 @@ import { IS_BILLING_ENABLED } from "@/ee/features/billing/stripe";
 import { redirect } from "next/navigation";
 import { auth } from "@/auth";
 import { isServiceError } from "@/lib/utils";
-import { getMe, getOrgAccountRequests } from "@/actions";
+import { getConnectionStats, getMe, getOrgAccountRequests } from "@/actions";
 import { ServiceErrorException } from "@/lib/serviceError";
 import { getOrgFromDomain } from "@/data/org";
 import { OrgRole } from "@prisma/client";
@@ -63,6 +63,11 @@ export default async function SettingsLayout(
         numJoinRequests = requests.length;
     }
 
+    const connectionStats = await getConnectionStats();
+    if (isServiceError(connectionStats)) {
+        throw new ServiceErrorException(connectionStats);
+    }
+
     const sidebarNavItems: SidebarNavItem[] = [
         {
             title: "General",
@@ -98,6 +103,7 @@ export default async function SettingsLayout(
                 title: "Connections",
                 href: `/${domain}/settings/connections`,
                 hrefRegex: `/${domain}/settings/connections(\/[^/]+)?$`,
+                isNotificationDotVisible: connectionStats.numberOfConnectionsWithFirstTimeSyncJobsInProgress > 0,
             }
         ] : []),
         {
@@ -140,4 +146,5 @@ export default async function SettingsLayout(
             </main>
         </div>
     )
-}
\ No newline at end of file
+}
+