diff --git a/src/support/slack/commands/add-repo.js b/src/support/slack/commands/add-repo.js
index a82bed3a7..0afaefd9a 100644
--- a/src/support/slack/commands/add-repo.js
+++ b/src/support/slack/commands/add-repo.js
@@ -38,7 +38,7 @@ function AddRepoCommand(context) {
     name: 'Add GitHub Repo',
     description: 'Adds a Github repository to previously added site.',
     phrases: PHRASES,
-    usageText: `${PHRASES.join(' or ')} {site} {githubRepoURL}`,
+    usageText: `${PHRASES.join(' or ')} {site} {githubRepoURL} [branch]`,
   });
 
   const { dataAccess, log } = context;
@@ -68,6 +68,25 @@ function AddRepoCommand(context) {
     }
   }
 
+  async function isOnboardedWithAemy(owner, repo) {
+    const { AEMY_BASE_URL } = process.env;
+    if (!AEMY_BASE_URL) {
+      throw new Error('AEMY_BASE_URL is not set');
+    }
+    const AEMY_ENDPOINT = `${AEMY_BASE_URL}/api/fn-ghapp/functions/get_installation_token/${owner}/${repo}`;
+    try {
+      const response = await fetch(AEMY_ENDPOINT, { headers: { 'x-api-key': process.env.AEMY_API_KEY } });
+      if (response.ok) {
+        const data = await response.json();
+        return !!data.token;
+      } else {
+        throw new Error('Failed to check if repository is onboarded with Aemy');
+      }
+    } catch (error) {
+      throw new Error(`Failed to check if repository is onboarded with Aemy: ${error.message}`);
+    }
+  }
+
   /**
    * Execute function for AddRepoCommand. This function validates the input, fetches the repository
    * information from the GitHub API, and saves it as a site in the database.
@@ -81,7 +100,7 @@ function AddRepoCommand(context) {
     const { say } = slackContext;
 
     try {
-      const [baseURLInput, repoUrlInput] = args;
+      const [baseURLInput, repoUrlInput, branchInput] = args;
 
       const baseURL = extractURLFromSlackInput(baseURLInput);
       let repoUrl = extractURLFromSlackInput(repoUrlInput, false, false);
@@ -106,22 +125,38 @@ function AddRepoCommand(context) {
 
       const repoInfo = await fetchRepoInfo(repoUrl);
 
+      let owner;
+      let repoName;
+      let branch;
+
       if (repoInfo === null) {
-        await say(`:warning: The GitHub repository '${repoUrl}' could not be found (private repo?).`);
-        return;
+        [owner, repoName] = repoUrl.split('github.com/')[1].split('/');
+        branch = branchInput || 'main';
+
+        await say(`:warning: GitHub API returned 404 for ${repoUrl}. Adding as private repo with branch: ${branch}`);
+      } else {
+        if (repoInfo.archived) {
+          await say(`:warning: The GitHub repository '${repoUrl}' is archived. Please unarchive it before adding it to a site.`);
+          return;
+        }
+
+        owner = repoInfo.owner.login;
+        repoName = repoInfo.name;
+        branch = branchInput || repoInfo.default_branch;
       }
 
-      if (repoInfo.archived) {
-        await say(`:warning: The GitHub repository '${repoUrl}' is archived. Please unarchive it before adding it to a site.`);
+      const isOnboarded = await isOnboardedWithAemy(owner, repoName);
+      if (!isOnboarded) {
+        await say(`:warning: The repository '${repoUrl}' is not onboarded with Aemy. Please onboard it with Aemy before adding it to a site.`);
         return;
       }
 
       site.setGitHubURL(repoUrl);
       const codeConfig = {
         type: 'github',
-        owner: repoInfo.owner.login,
-        repo: repoInfo.name,
-        ref: repoInfo.default_branch,
+        owner,
+        repo: repoName,
+        ref: branch,
         url: repoUrl,
       };
       site.setCode(codeConfig);
diff --git a/test/support/slack/commands/add-repo.test.js b/test/support/slack/commands/add-repo.test.js
index 6febd553a..d789aba56 100644
--- a/test/support/slack/commands/add-repo.test.js
+++ b/test/support/slack/commands/add-repo.test.js
@@ -24,8 +24,15 @@ describe('AddRepoCommand', () => {
   let dataAccessStub;
   let sqsStub;
   let siteStub;
+  const AEMY_BASE_URL = 'https://test-aemy-base-url.net';
+
+  // Helper function to construct Aemy API endpoint path
+  const getAemyEndpointPath = (owner, repo) => `/api/fn-ghapp/functions/get_installation_token/${owner}/${repo}`;
 
   beforeEach(() => {
+    process.env.AEMY_API_KEY = 'test-api-key';
+    process.env.AEMY_BASE_URL = AEMY_BASE_URL;
+
     sqsStub = {
       sendMessage: sinon.stub().resolves(),
     };
@@ -94,11 +101,16 @@ describe('AddRepoCommand', () => {
           default_branch: 'main',
         });
 
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: 'some-token' });
+
       const args = ['validSite.com', 'https://github.com/valid/repo'];
       const command = AddRepoCommand(context);
 
       await command.handleExecution(args, slackContext);
 
+      expect(aemyScope.isDone()).to.be.true;
       expect(slackContext.say.called).to.be.true;
       expect(siteStub.setGitHubURL).to.have.been.calledWith('https://github.com/valid/repo');
       expect(siteStub.setCode).to.have.been.calledWith({
@@ -134,11 +146,17 @@ describe('AddRepoCommand', () => {
           default_branch: 'main',
         });
 
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: 'some-token' });
+
       const args = ['validSite.com', 'github.com/valid/repo'];
       const command = AddRepoCommand(context);
 
       await command.handleExecution(args, slackContext);
 
+      expect(aemyScope.isDone()).to.be.true;
+
       expect(slackContext.say).calledWith('\n'
         + '      :white_check_mark: *GitHub repo added for <undefined|undefined>*\n'
         + '\n'
@@ -221,9 +239,14 @@ describe('AddRepoCommand', () => {
           default_branch: 'main',
         });
 
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: 'some-token' });
+
       await command.handleExecution(args, slackContext);
 
       // Assertions to confirm repo info was fetched and handled correctly
+      expect(aemyScope.isDone()).to.be.true;
       expect(slackContext.say).calledWithMatch(/GitHub repo added/);
       expect(siteStub.setCode).to.have.been.calledWith({
         type: 'github',
@@ -234,16 +257,36 @@ describe('AddRepoCommand', () => {
       });
     });
 
-    it('handles non-existent repository (404 error)', async () => {
+    it('handles private repo', async () => {
       nock('https://api.github.com')
-        .get('/repos/invalid/repo')
+        .get('/repos/private/repo')
         .reply(404);
 
-      args[1] = 'https://github.com/invalid/repo';
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('private', 'repo'))
+        .reply(200, { token: 'some-token' });
+
+      args[1] = 'https://github.com/private/repo';
       await command.handleExecution(args, slackContext);
 
-      // Assertions to confirm handling of non-existent repository
-      expect(slackContext.say.calledWith(':warning: The GitHub repository \'https://github.com/invalid/repo\' could not be found (private repo?).')).to.be.true;
+      // Should verify Aemy check was made
+      expect(aemyScope.isDone()).to.be.true;
+
+      // Should parse URL manually and add as private repo with 'main' branch
+      expect(siteStub.setCode).to.have.been.calledWith({
+        type: 'github',
+        owner: 'private',
+        repo: 'repo',
+        ref: 'main', // defaults to 'main' for private repos
+        url: 'https://github.com/private/repo',
+      });
+      expect(siteStub.save).to.have.been.called;
+
+      // Should send warning about adding as private repo
+      expect(slackContext.say.calledWithMatch(/GitHub API returned 404/)).to.be.true;
+      expect(slackContext.say.calledWithMatch(/Adding as private repo/)).to.be.true;
+      // Should send success message
+      expect(slackContext.say.calledWithMatch(/GitHub repo added/)).to.be.true;
     });
 
     it('handles errors other than 404 from GitHub API', async () => {
@@ -270,4 +313,238 @@ describe('AddRepoCommand', () => {
       expect(slackContext.say.calledWithMatch(/Network error occurred/)).to.be.true;
     });
   });
+
+  describe('Branch Support', () => {
+    it('handles custom branch for public repository', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: 'some-token' });
+
+      const args = ['validSite.com', 'https://github.com/valid/repo', 'develop'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyScope.isDone()).to.be.true;
+      expect(siteStub.setCode).to.have.been.calledWith({
+        type: 'github',
+        owner: 'valid',
+        repo: 'repo',
+        ref: 'develop', // Should use custom branch
+        url: 'https://github.com/valid/repo',
+      });
+      expect(siteStub.save).to.have.been.called;
+    });
+
+    it('handles custom branch for private repository', async () => {
+      nock('https://api.github.com')
+        .get('/repos/private/repo')
+        .reply(404);
+
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('private', 'repo'))
+        .reply(200, { token: 'some-token' });
+
+      const args = ['validSite.com', 'https://github.com/private/repo', 'feature-branch'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyScope.isDone()).to.be.true;
+      expect(slackContext.say.calledWithMatch(/GitHub API returned 404/)).to.be.true;
+      expect(slackContext.say.calledWithMatch(/Adding as private repo/)).to.be.true;
+      expect(slackContext.say.calledWithMatch(/feature-branch/)).to.be.true;
+      expect(siteStub.setCode).to.have.been.calledWith({
+        type: 'github',
+        owner: 'private',
+        repo: 'repo',
+        ref: 'feature-branch', // Should use custom branch
+        url: 'https://github.com/private/repo',
+      });
+      expect(siteStub.save).to.have.been.called;
+
+      // Should send success message
+      expect(slackContext.say.calledWithMatch(/GitHub repo added/)).to.be.true;
+    });
+
+    it('handles private repository without custom branch (defaults to main)', async () => {
+      nock('https://api.github.com')
+        .get('/repos/private/repo')
+        .reply(404);
+
+      const aemyScope = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('private', 'repo'))
+        .reply(200, { token: 'some-token' });
+
+      const args = ['validSite.com', 'https://github.com/private/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyScope.isDone()).to.be.true;
+      expect(siteStub.setCode).to.have.been.calledWith({
+        type: 'github',
+        owner: 'private',
+        repo: 'repo',
+        ref: 'main', // Should default to 'main' for private repos
+        url: 'https://github.com/private/repo',
+      });
+      expect(siteStub.save).to.have.been.called;
+    });
+  });
+
+  describe('Aemy Integration', () => {
+    it('throws error when AEMY_BASE_URL is not set', async () => {
+      delete process.env.AEMY_BASE_URL;
+
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(slackContext.say.calledWithMatch(/AEMY_BASE_URL is not set/)).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+
+      // Restore for subsequent tests
+      process.env.AEMY_BASE_URL = AEMY_BASE_URL;
+    });
+
+    it('blocks repository not onboarded with Aemy (token is null)', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyNock = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: null });
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyNock.isDone()).to.be.true;
+      expect(slackContext.say.calledWith(':warning: The repository \'https://github.com/valid/repo\' is not onboarded with Aemy. Please onboard it with Aemy before adding it to a site.')).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+    });
+
+    it('blocks repository not onboarded with Aemy (token is empty string)', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyNock = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, { token: '' });
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyNock.isDone()).to.be.true;
+      expect(slackContext.say.calledWith(':warning: The repository \'https://github.com/valid/repo\' is not onboarded with Aemy. Please onboard it with Aemy before adding it to a site.')).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+    });
+
+    it('blocks repository not onboarded with Aemy (token is undefined)', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyNock = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(200, {});
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyNock.isDone()).to.be.true;
+      expect(slackContext.say.calledWith(':warning: The repository \'https://github.com/valid/repo\' is not onboarded with Aemy. Please onboard it with Aemy before adding it to a site.')).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+    });
+
+    it('handles Aemy API error responses', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyNock = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .reply(500, { error: 'Internal Server Error' });
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyNock.isDone()).to.be.true;
+      expect(slackContext.say.calledWithMatch(/Failed to check if repository is onboarded with Aemy/)).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+    });
+
+    it('handles Aemy API network errors', async () => {
+      nock('https://api.github.com')
+        .get('/repos/valid/repo')
+        .reply(200, {
+          archived: false,
+          name: 'repo',
+          owner: { login: 'valid' },
+          default_branch: 'main',
+        });
+
+      const aemyNock = nock(AEMY_BASE_URL)
+        .get(getAemyEndpointPath('valid', 'repo'))
+        .replyWithError('Network error');
+
+      const args = ['validSite.com', 'https://github.com/valid/repo'];
+      const command = AddRepoCommand(context);
+
+      await command.handleExecution(args, slackContext);
+
+      expect(aemyNock.isDone()).to.be.true;
+      expect(slackContext.say.calledWithMatch(/Network error/)).to.be.true;
+      expect(siteStub.save).to.not.have.been.called;
+    });
+  });
 });