diff --git a/jupytext/jupytext.py b/jupytext/jupytext.py
index 22ad128dc..5ff6cca28 100644
--- a/jupytext/jupytext.py
+++ b/jupytext/jupytext.py
@@ -95,7 +95,7 @@ def writes(self, nb, **kwargs):
 
         for cell in nb.cells:
             if looking_for_first_markdown_cell and cell.cell_type == 'markdown':
-                cell.metadata['cell_marker'] = '"""'
+                cell.metadata.setdefault('cell_marker', '"""')
                 looking_for_first_markdown_cell = False
 
             cell_exporters.append(self.format.cell_exporter_class(