diff --git a/.github/workflows/auto-fill-pr.yml b/.github/workflows/auto-fill-pr.yml
index e8351bb..42e7b66 100644
--- a/.github/workflows/auto-fill-pr.yml
+++ b/.github/workflows/auto-fill-pr.yml
@@ -234,9 +234,17 @@ jobs:
               const sectionRegex = new RegExp(`## ${sectionHeader}\\s*([\\s\\S]*?)(?=\\n## |$)`, 'i');
               const match = body.match(sectionRegex);
               if (!match) return true;
-              const content = match[1].trim();
-              // Empty if only whitespace, empty, or just an HTML comment
-              return !content || /^<!--.*-->$/.test(content);
+              // Strip noise that doesn't count as user content:
+              // - HTML comments (template placeholders)
+              // - Reference-style link definitions added by Jira/GitHub integrations (e.g. [IM-123]: https://...)
+              // - Horizontal rules and our own footer markers (from previous workflow runs)
+              const content = match[1]
+                .replace(/<!--[\s\S]*?-->/g, '')
+                .replace(/^\[.+?\]:\s*\S.*$/gm, '')
+                .replace(/^[-*]{3,}$/gm, '')
+                .replace(/^_.*Auto-(generated|filled).*_$/gm, '')
+                .trim();
+              return !content;
             };
 
             // Helper to check if any checkbox is checked in Type of Change
@@ -334,7 +342,7 @@ jobs:
             // Add footer if we changed anything
             const madeChanges = fillDescription || (fillTicket && ticketSection) || fillType || (fillTesting && testing);
             if (madeChanges && !newBody.includes('Auto-generated by Claude') && !newBody.includes('Auto-filled')) {
-              const footer = claudeSuccess ? '\n\n---\n_✨ Auto-generated by Claude_' : '\n\n---\n_📝 Auto-filled_';
+              const footer = claudeSuccess ? '\n\n***\n_✨ Auto-generated by Claude_' : '\n\n***\n_📝 Auto-filled_';
               newBody = newBody.trim() + footer;
             }