diff --git a/apps/server/agent/cleanup-manager.ts b/apps/server/agent/cleanup-manager.ts
index cb8b1ff..f93c5c4 100644
--- a/apps/server/agent/cleanup-manager.ts
+++ b/apps/server/agent/cleanup-manager.ts
@@ -297,7 +297,7 @@ export class CleanupManager {
 
   /**
    * Auto-cleanup agent workdir after successful completion.
-   * Removes worktrees and logs but preserves branches and DB record.
+   * Removes worktrees, branches, and logs. Preserves DB record.
    */
   async autoCleanupAfterCompletion(
     agentId: string,
@@ -320,10 +320,18 @@ export class CleanupManager {
       await this.archiveForDebug(alias, agentId);
     }
 
+    let worktreeRemoved = true;
     try {
       await this.removeAgentWorktrees(alias, initiativeId);
     } catch (err) {
       log.warn({ agentId, alias, err: err instanceof Error ? err.message : String(err) }, 'auto-cleanup: failed to remove worktrees');
+      worktreeRemoved = false;
+    }
+
+    try {
+      await this.removeAgentBranches(alias, initiativeId);
+    } catch (err) {
+      log.warn({ agentId, alias, err: err instanceof Error ? err.message : String(err) }, 'auto-cleanup: failed to remove branches');
     }
 
     try {
@@ -333,7 +341,7 @@ export class CleanupManager {
     }
 
     log.info({ agentId, alias }, 'auto-cleanup: workdir and logs removed');
-    return { clean: true, removed: true };
+    return { clean: true, removed: worktreeRemoved };
   }
 
   /**
diff --git a/apps/server/agent/manager.ts b/apps/server/agent/manager.ts
index 6c62c0d..5065e91 100644
--- a/apps/server/agent/manager.ts
+++ b/apps/server/agent/manager.ts
@@ -855,6 +855,17 @@ export class MultiProviderAgentManager implements AgentManager {
     log.info({ agentId, name: agent.name }, 'dismissing agent');
 
     this.cleanupAgentState(agentId);
+    this.commitRetryCount.delete(agentId);
+
+    // Best-effort filesystem cleanup
+    try { await this.cleanupManager.removeAgentWorktrees(agent.name, agent.initiativeId); }
+    catch (err) { log.warn({ agentId, err: err instanceof Error ? err.message : String(err) }, 'dismiss: failed to remove worktrees'); }
+
+    try { await this.cleanupManager.removeAgentBranches(agent.name, agent.initiativeId); }
+    catch (err) { log.warn({ agentId, err: err instanceof Error ? err.message : String(err) }, 'dismiss: failed to remove branches'); }
+
+    try { await this.cleanupManager.removeAgentLogs(agent.name); }
+    catch (err) { log.warn({ agentId, err: err instanceof Error ? err.message : String(err) }, 'dismiss: failed to remove logs'); }
 
     await this.repository.update(agentId, {
       userDismissedAt: new Date(),