diff --git a/packages/cli/src/commands/workflow.test.ts b/packages/cli/src/commands/workflow.test.ts
index 7f13f8d83f..53a825e1f8 100644
--- a/packages/cli/src/commands/workflow.test.ts
+++ b/packages/cli/src/commands/workflow.test.ts
@@ -867,6 +867,41 @@ describe('workflowRunCommand', () => {
     expect(createCallsAfter).toBe(createCallsBefore);
   });
 
+  it('surfaces auto-registration failures instead of claiming the repo is invalid', async () => {
+    const { discoverWorkflowsWithConfig } = await import('@archon/workflows/workflow-discovery');
+    const { registerRepository } = await import('@archon/core');
+    const conversationDb = await import('@archon/core/db/conversations');
+    const codebaseDb = await import('@archon/core/db/codebases');
+    const gitModule = await import('@archon/git');
+
+    (discoverWorkflowsWithConfig as ReturnType<typeof mock>).mockResolvedValueOnce({
+      workflows: [makeTestWorkflowWithSource({ name: 'assist', description: 'Help' })],
+      errors: [],
+    });
+    (conversationDb.getOrCreateConversation as ReturnType<typeof mock>).mockResolvedValueOnce({
+      id: 'conv-123',
+    });
+    (codebaseDb.findCodebaseByDefaultCwd as ReturnType<typeof mock>).mockResolvedValueOnce(null);
+    (gitModule.findRepoRoot as ReturnType<typeof mock>).mockResolvedValueOnce('/test/path');
+    (registerRepository as ReturnType<typeof mock>).mockRejectedValueOnce(
+      new Error(
+        'Source symlink at /home/test/.archon/workspaces/acme/widget/source already points to ' +
+          '/home/test/.archon/workspaces/widget, expected /test/path'
+      )
+    );
+
+    const error = await workflowRunCommand('/test/path', 'assist', 'hello', {}).catch(
+      err => err as Error
+    );
+
+    expect(error).toBeInstanceOf(Error);
+    expect(error.message).toContain('Cannot create worktree: repository registration failed.');
+    expect(error.message).toContain(
+      'Remove the stale workspace entry at /home/test/.archon/workspaces/acme/widget and retry'
+    );
+    expect(error.message).not.toContain('not in a git repository');
+  });
+
   it('throws when isolation cannot be created due to missing codebase', async () => {
     const { discoverWorkflowsWithConfig } = await import('@archon/workflows/workflow-discovery');
     const conversationDb = await import('@archon/core/db/conversations');
diff --git a/packages/cli/src/commands/workflow.ts b/packages/cli/src/commands/workflow.ts
index 6ba31d1256..688e219619 100644
--- a/packages/cli/src/commands/workflow.ts
+++ b/packages/cli/src/commands/workflow.ts
@@ -21,6 +21,7 @@ import {
 } from '@archon/workflows/event-emitter';
 import type { WorkflowLoadResult } from '@archon/workflows/schemas/workflow';
 import type { WorkflowRun } from '@archon/workflows/schemas/workflow-run';
+import { join } from 'node:path';
 import {
   approveWorkflow,
   rejectWorkflow,
@@ -77,6 +78,31 @@ function generateConversationId(): string {
   return `cli-${String(timestamp)}-${random}`;
 }
 
+function extractStaleWorkspaceEntry(message: string): string | null {
+  const prefix = 'Source symlink at ';
+  const delimiter = ' already points to ';
+  if (!message.startsWith(prefix)) return null;
+
+  const remainder = message.slice(prefix.length);
+  const delimiterIndex = remainder.indexOf(delimiter);
+  if (delimiterIndex === -1) return null;
+
+  const sourcePath = remainder.slice(0, delimiterIndex).trim();
+  const lastSeparator = Math.max(sourcePath.lastIndexOf('/'), sourcePath.lastIndexOf('\\'));
+  return lastSeparator === -1 ? null : sourcePath.slice(0, lastSeparator);
+}
+
+function buildRegistrationFailureError(action: string, error: Error): Error {
+  const staleWorkspaceEntry = extractStaleWorkspaceEntry(error.message);
+  const hint = staleWorkspaceEntry
+    ? `Hint: Remove the stale workspace entry at ${staleWorkspaceEntry} and retry, or use --no-worktree to skip isolation.`
+    : `Hint: Check your Archon workspace registration under ${join(getArchonHome(), 'workspaces')} and retry, or use --no-worktree to skip isolation.`;
+
+  return new Error(
+    `Cannot ${action}: repository registration failed.\n` + `Error: ${error.message}\n` + hint
+  );
+}
+
 /** Render a workflow event to stderr as a progress line. Called only when --quiet is not set. */
 function renderWorkflowEvent(event: WorkflowEmitterEvent, verbose: boolean): void {
   switch (event.type) {
@@ -285,6 +311,7 @@ export async function workflowRunCommand(
   // Try to find a codebase for this directory
   let codebase = null;
   let codebaseLookupError: Error | null = null;
+  let codebaseRegistrationError: Error | null = null;
   try {
     codebase = await codebaseDb.findCodebaseByDefaultCwd(cwd);
   } catch (error) {
@@ -330,6 +357,7 @@ export async function workflowRunCommand(
         }
       } catch (error) {
         const err = error as Error;
+        codebaseRegistrationError = err;
         getLog().warn(
           { err, errorType: err.constructor.name, repoRoot },
           'cli.codebase_auto_registration_failed'
@@ -354,6 +382,9 @@ export async function workflowRunCommand(
             'Hint: Check your database connection before using --resume.'
         );
       }
+      if (codebaseRegistrationError) {
+        throw buildRegistrationFailureError('resume', codebaseRegistrationError);
+      }
       throw new Error(
         'Cannot resume: Not in a git repository.\n' +
           'Either run from a git repo or use /clone first.'
@@ -507,6 +538,9 @@ export async function workflowRunCommand(
           'Hint: Check your database connection, or use --no-worktree to skip isolation.'
       );
     }
+    if (codebaseRegistrationError) {
+      throw buildRegistrationFailureError('create worktree', codebaseRegistrationError);
+    }
     throw new Error(
       'Cannot create worktree: not in a git repository.\n' +
         'Run from within a git repo, or use --no-worktree to skip isolation.'