diff --git a/CHANGELOG.md b/CHANGELOG.md
index e30b290c47..d3ce6b1811 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### General
 
 - Fix `blog_post` parameter for `nf-core pipelines sync` command ([#3911](https://github.com/nf-core/tools/pull/3911))
+- Fix markdown in sync PR message ([#3913](https://github.com/nf-core/tools/pull/3913))
 
 ## [v3.5.0 - Terne Topi](https://github.com/nf-core/tools/releases/tag/3.5.0) - [2025-11-19]
 
diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 33fa4674ee..f361d1cbe8 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -421,7 +421,7 @@ def make_pull_request(self):
             "[https://nf-co.re/docs/contributing/sync/](https://nf-co.re/docs/contributing/sync/#merging-automated-prs).\n\n"
             "For more information about this release of [nf-core/tools](https://github.com/nf-core/tools), "
             "please see the `v{tag}` [release page](https://github.com/nf-core/tools/releases/tag/{tag})."
-            "> [!NOTE]\n"
+            "\n\n> [!NOTE]\n"
             "> Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository."
             "Older template PRs will be automatically closed once a newer template PR has been merged."
         ).format(tag=nf_core.__version__)