diff --git a/src/entrypoints/run.ts b/src/entrypoints/run.ts
index 4a57395..1848603 100644
--- a/src/entrypoints/run.ts
+++ b/src/entrypoints/run.ts
@@ -229,8 +229,8 @@ async function run() {
     // Restore them from the base branch before the CLI reads them.
     //
     // We read pull_request.base.ref from the payload directly because agent
-    // mode's branchInfo.baseBranch defaults to "main" rather than the PR's
-    // actual target (agent/index.ts). For issue_comment on a PR the payload
+    // mode's branchInfo.baseBranch defaults to the repo's default branch rather
+    // than the PR's actual target (agent/index.ts). For issue_comment on a PR the payload
     // lacks base.ref, so we fall back to the mode-provided value — tag mode
     // fetches it from GraphQL; agent mode on issue_comment is an edge case
     // that at worst restores from the wrong trusted branch (still secure).
@@ -312,7 +312,7 @@ async function run() {
           commentId,
           githubToken,
           claudeBranch,
-          baseBranch: baseBranch || "main",
+          baseBranch: baseBranch || context.repository.default_branch || "main",
           triggerUsername: context.actor,
           context,
           octokit,
diff --git a/src/entrypoints/update-comment-link.ts b/src/entrypoints/update-comment-link.ts
index c7bd8d6..c0963e8 100644
--- a/src/entrypoints/update-comment-link.ts
+++ b/src/entrypoints/update-comment-link.ts
@@ -253,7 +253,8 @@ async function run() {
       commentId: parseInt(process.env.CLAUDE_COMMENT_ID!),
       githubToken,
       claudeBranch: process.env.CLAUDE_BRANCH,
-      baseBranch: process.env.BASE_BRANCH || "main",
+      baseBranch:
+        process.env.BASE_BRANCH || context.repository.default_branch || "main",
       triggerUsername: process.env.TRIGGER_USERNAME,
       context,
       octokit,
diff --git a/src/github/context.ts b/src/github/context.ts
index a0b388c..eeefb99 100644
--- a/src/github/context.ts
+++ b/src/github/context.ts
@@ -79,6 +79,7 @@ type BaseContext = {
     owner: string;
     repo: string;
     full_name: string;
+    default_branch?: string;
   };
   actor: string;
   inputs: {
@@ -140,6 +141,7 @@ export function parseGitHubContext(): GitHubContext {
       owner: context.repo.owner,
       repo: context.repo.repo,
       full_name: `${context.repo.owner}/${context.repo.repo}`,
+      default_branch: context.payload.repository?.default_branch,
     },
     actor: context.actor,
     inputs: {
diff --git a/src/modes/agent/index.ts b/src/modes/agent/index.ts
index e604737..b648716 100644
--- a/src/modes/agent/index.ts
+++ b/src/modes/agent/index.ts
@@ -85,15 +85,15 @@ export async function prepareAgentMode({
 
   // Check for branch info from environment variables (useful for auto-fix workflows)
   const claudeBranch = process.env.CLAUDE_BRANCH || undefined;
-  const baseBranch =
-    process.env.BASE_BRANCH || context.inputs.baseBranch || "main";
+  const defaultBranch = context.repository.default_branch || "main";
+  const baseBranch = context.inputs.baseBranch || defaultBranch;
 
   // Detect current branch from GitHub environment
   const currentBranch =
     claudeBranch ||
     process.env.GITHUB_HEAD_REF ||
     process.env.GITHUB_REF_NAME ||
-    "main";
+    defaultBranch;
 
   // Get our GitHub MCP servers config
   const ourMcpConfig = await prepareMcpConfig({
diff --git a/test/mockContext.ts b/test/mockContext.ts
index c02caa4..324104e 100644
--- a/test/mockContext.ts
+++ b/test/mockContext.ts
@@ -36,6 +36,7 @@ const defaultRepository = {
   owner: "test-owner",
   repo: "test-repo",
   full_name: "test-owner/test-repo",
+  default_branch: "main",
 };
 
 type MockContextOverrides = Omit<Partial<ParsedGitHubContext>, "inputs"> & {
diff --git a/test/modes/agent.test.ts b/test/modes/agent.test.ts
index be6f0d2..1404b0d 100644
--- a/test/modes/agent.test.ts
+++ b/test/modes/agent.test.ts
@@ -88,7 +88,7 @@ describe("Agent Mode", () => {
     expect(result.claudeArgs).toBe("--model claude-sonnet-4 --max-turns 10");
     expect(result.claudeArgs).not.toContain("--mcp-config");
 
-    // Verify return structure - should use "main" as fallback when no env vars set
+    // Verify return structure - should fall back to repository.default_branch when no env vars set
     expect(result).toEqual({
       commentId: undefined,
       branchInfo: {
@@ -108,6 +108,60 @@ describe("Agent Mode", () => {
       process.env.GITHUB_REF_NAME = originalRefName;
   });
 
+  test("prepare falls back to repository.default_branch when not 'main'", async () => {
+    const contextWithDevelop = createMockAutomationContext({
+      eventName: "workflow_dispatch",
+      repository: {
+        owner: "test-owner",
+        repo: "test-repo",
+        full_name: "test-owner/test-repo",
+        default_branch: "develop",
+      },
+    });
+
+    // Save and clear env vars that would otherwise override the fallback
+    const originalClaudeBranch = process.env.CLAUDE_BRANCH;
+    const originalHeadRef = process.env.GITHUB_HEAD_REF;
+    const originalRefName = process.env.GITHUB_REF_NAME;
+    delete process.env.CLAUDE_BRANCH;
+    delete process.env.GITHUB_HEAD_REF;
+    delete process.env.GITHUB_REF_NAME;
+
+    const mockOctokit = {
+      rest: {
+        users: {
+          getAuthenticated: mock(() =>
+            Promise.resolve({
+              data: { login: "test-user", id: 12345, type: "User" },
+            }),
+          ),
+          getByUsername: mock(() =>
+            Promise.resolve({
+              data: { login: "test-user", id: 12345, type: "User" },
+            }),
+          ),
+        },
+      },
+    } as any;
+
+    const result = await prepareAgentMode({
+      context: contextWithDevelop,
+      octokit: mockOctokit,
+      githubToken: "test-token",
+    });
+
+    expect(result.branchInfo.baseBranch).toBe("develop");
+    expect(result.branchInfo.currentBranch).toBe("develop");
+
+    // Restore env vars
+    if (originalClaudeBranch !== undefined)
+      process.env.CLAUDE_BRANCH = originalClaudeBranch;
+    if (originalHeadRef !== undefined)
+      process.env.GITHUB_HEAD_REF = originalHeadRef;
+    if (originalRefName !== undefined)
+      process.env.GITHUB_REF_NAME = originalRefName;
+  });
+
   test("prepare rejects bot actors without allowed_bots", async () => {
     const contextWithPrompts = createMockAutomationContext({
       eventName: "workflow_dispatch",