diff --git a/.github/workflows/check-untracked-repos.yml b/.github/workflows/check-untracked-repos.yml
new file mode 100644
index 000000000..85c37d027
--- /dev/null
+++ b/.github/workflows/check-untracked-repos.yml
@@ -0,0 +1,23 @@
+name: Check Untracked Repositories
+
+on:
+  schedule:
+    - cron: '0 */6 * * *'
+  workflow_dispatch:
+
+jobs:
+  check-untracked-repos:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+
+      - name: Install Rust stable
+        uses: ./.github/actions/setup-rust
+
+      - name: Check for untracked repositories
+        shell: bash
+        run: |
+          cargo build --release
+          ./target/release/rust-team ci check-untracked-repos
diff --git a/.github/workflows/dry-run.yml b/.github/workflows/dry-run.yml
index 965d983d2..9b148aed8 100644
--- a/.github/workflows/dry-run.yml
+++ b/.github/workflows/dry-run.yml
@@ -111,4 +111,4 @@ jobs:
           echo "Pull request ${PR}"
           gh pr comment ${PR} --repo rust-lang/team --body-file comment.txt \
             --edit-last \
-            --create-if-none
+            --create-if-none
\ No newline at end of file
diff --git a/src/api/github.rs b/src/api/github.rs
index 8945ebb85..859f39fad 100644
--- a/src/api/github.rs
+++ b/src/api/github.rs
@@ -116,6 +116,17 @@ impl GitHubApi {
             .json()?)
     }
 
+    pub(crate) fn get<T>(&self, url: &str) -> Result<T, Error>
+    where
+        T: serde::de::DeserializeOwned,
+    {
+        Ok(self
+            .prepare(false, Method::GET, url)?
+            .send()?
+            .error_for_status()?
+            .json()?)
+    }
+
     pub(crate) fn usernames(&self, ids: &[u64]) -> Result<HashMap<u64, String>, Error> {
         #[derive(serde::Deserialize)]
         #[serde(rename_all = "camelCase")]
diff --git a/src/ci.rs b/src/ci.rs
index 4ae611b64..c27f2c53f 100644
--- a/src/ci.rs
+++ b/src/ci.rs
@@ -1,7 +1,8 @@
 use crate::data::Data;
 use crate::schema::RepoPermission;
-use anyhow::Context;
-use std::collections::BTreeSet;
+use anyhow::{bail, Context};
+use log::{debug, info, warn};
+use std::collections::{BTreeSet, HashSet};
 use std::path::{Path, PathBuf};
 
 /// Generates the contents of `.github/CODEOWNERS`, based on
@@ -170,3 +171,134 @@ fn codeowners_path() -> PathBuf {
         .join(".github")
         .join("CODEOWNERS")
 }
+
+#[derive(Debug, serde::Deserialize)]
+struct GitHubRepo {
+    name: String,
+    archived: bool,
+    fork: bool,
+}
+
+#[derive(Debug)]
+struct UntrackedRepo {
+    org: String,
+    name: String,
+}
+
+/// Check for untracked repositories and fail if any are found
+pub fn check_untracked_repos(data: &Data) -> anyhow::Result<()> {
+    let github = crate::api::github::GitHubApi::new();
+
+    // Get allowed GitHub organizations from config instead of hardcoding
+    let orgs_to_monitor: Vec<&str> = data
+        .config()
+        .allowed_github_orgs()
+        .iter()
+        .filter(|org| {
+            // Exclude independent orgs that shouldn't be synchronized
+            !data
+                .config()
+                .independent_github_orgs()
+                .contains(org.as_str())
+        })
+        .map(|s| s.as_str())
+        .collect();
+
+    info!(
+        "🔍 Checking for untracked repositories in organizations: {}",
+        orgs_to_monitor.join(", ")
+    );
+
+    info!("Fetching repositories from GitHub...");
+    let github_repos = fetch_all_github_repos(&github, &orgs_to_monitor)?;
+    info!(
+        "Found {} total repositories in GitHub organizations",
+        github_repos.len()
+    );
+
+    info!("Parsing local TOML files...");
+    let tracked_repos = parse_tracked_repos(data);
+    info!(
+        "Found {} tracked repositories in repos/ directory",
+        tracked_repos.len()
+    );
+
+    info!("Comparing GitHub repos with tracked repos...");
+    let untracked = find_untracked_repos(&github_repos, &tracked_repos);
+
+    if untracked.is_empty() {
+        info!("✅ All repositories are tracked!");
+        return Ok(());
+    }
+
+    warn!("❌ Found {} untracked repositories:", untracked.len());
+    for repo in &untracked {
+        warn!("  - {}/{}", repo.org, repo.name);
+    }
+
+    bail!(
+        "Found {} untracked repositories. Please add them to the repos/ directory.",
+        untracked.len()
+    );
+}
+
+fn fetch_all_github_repos(
+    github: &crate::api::github::GitHubApi,
+    orgs_to_monitor: &[&str],
+) -> anyhow::Result<Vec<(String, GitHubRepo)>> {
+    let mut all_repos = Vec::new();
+
+    for org in orgs_to_monitor {
+        debug!("Fetching repos for org: {}", org);
+        let mut page = 1;
+
+        loop {
+            let url = format!("orgs/{}/repos?per_page=100&page={}", org, page);
+
+            let repos: Vec<GitHubRepo> = github
+                .get(&url)
+                .with_context(|| format!("Failed to fetch repos for org: {}", org))?;
+
+            if repos.is_empty() {
+                break;
+            }
+
+            for repo in repos {
+                all_repos.push((org.to_string(), repo));
+            }
+
+            page += 1;
+        }
+    }
+
+    Ok(all_repos)
+}
+
+fn parse_tracked_repos(data: &Data) -> HashSet<(String, String)> {
+    data.all_repos()
+        .map(|repo| (repo.org.clone(), repo.name.clone()))
+        .collect()
+}
+
+fn find_untracked_repos(
+    github_repos: &[(String, GitHubRepo)],
+    tracked_repos: &HashSet<(String, String)>,
+) -> Vec<UntrackedRepo> {
+    github_repos
+        .iter()
+        .filter(|(org, repo)| {
+            // Skip forks
+            if repo.fork {
+                debug!("Skipping fork: {}/{}", org, repo.name);
+                return false;
+            }
+
+            // Check if tracked
+            !tracked_repos.contains(&(org.clone(), repo.name.clone()))
+        })
+        .map(|(org, repo)| UntrackedRepo {
+            org: org.clone(),
+            name: repo.name.clone(),
+        })
+        .collect()
+}
diff --git a/src/main.rs b/src/main.rs
index 3e09d8b69..b7bd2909f 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -115,6 +115,8 @@ enum CiOpts {
     GenerateCodeowners,
     /// Check if the .github/CODEOWNERS file is up-to-date
     CheckCodeowners,
+    /// Check for untracked repositories in GitHub organizations
+    CheckUntrackedRepos,
 }
 
 #[derive(clap::Parser, Debug)]
@@ -535,6 +537,7 @@ fn run() -> Result<(), Error> {
         Cli::Ci(opts) => match opts {
             CiOpts::GenerateCodeowners => generate_codeowners_file(data)?,
             CiOpts::CheckCodeowners => check_codeowners(data)?,
+            CiOpts::CheckUntrackedRepos => ci::check_untracked_repos(&data)?,
         },
         Cli::Sync(opts) => {
             if let Err(err) = perform_sync(opts, data) {