diff --git a/jupytext/metadata_filter.py b/jupytext/metadata_filter.py
index c4d80cb8a..fecb28ab8 100644
--- a/jupytext/metadata_filter.py
+++ b/jupytext/metadata_filter.py
@@ -92,6 +92,18 @@ def update_metadata_filters(metadata, jupyter_md, cell_metadata):
         cell_metadata = {'additional': cell_metadata, 'excluded': 'all'}
         metadata.setdefault('jupytext', {})['notebook_metadata_filter'] = '-all'
         metadata.setdefault('jupytext', {})['cell_metadata_filter'] = metadata_filter_as_string(cell_metadata)
+    else:
+        # Update the notebook metadata filter to include existing entries 376
+        nb_md_filter = metadata.get('jupytext', {}).get('notebook_metadata_filter', '').split(',')
+        nb_md_filter = [key for key in nb_md_filter if key]
+        if 'all' in nb_md_filter or '-all' in nb_md_filter:
+            return
+        for key in metadata:
+            if key in _DEFAULT_NOTEBOOK_METADATA or key in nb_md_filter or ('-' + key) in nb_md_filter:
+                continue
+            nb_md_filter.append(key)
+        if nb_md_filter:
+            metadata.setdefault('jupytext', {})['notebook_metadata_filter'] = ','.join(nb_md_filter)
 
 
 def apply_metadata_filters(user_filter, default_filter, actual_keys):
diff --git a/tests/test_read_simple_markdown.py b/tests/test_read_simple_markdown.py
index 8e9c38e46..711206b6f 100644
--- a/tests/test_read_simple_markdown.py
+++ b/tests/test_read_simple_markdown.py
@@ -595,9 +595,9 @@ def test_two_markdown_cell_with_no_language_code_works(nb=new_notebook(cells=[
 def test_notebook_with_python3_magic(no_jupytext_version_number,
                                      nb=new_notebook(metadata={
                                          'kernelspec': {'display_name': 'Python 3', 'language': 'python',
-                                                        'name': 'python3'}},
-                                                     cells=[new_code_cell('%%python2\na = 1\nprint a'),
-                                                            new_code_cell('%%python3\nb = 2\nprint(b)')]),
+                                                        'name': 'python3'}}, cells=[
+                                         new_code_cell('%%python2\na = 1\nprint a'),
+                                         new_code_cell('%%python3\nb = 2\nprint(b)')]),
                                      text="""---
 jupyter:
   kernelspec:
@@ -621,3 +621,59 @@ def test_notebook_with_python3_magic(no_jupytext_version_number,
 
     nb2 = jupytext.reads(md, 'md')
     compare_notebooks(nb2, nb)
+
+
+def test_update_metadata_filter(
+        no_jupytext_version_number,
+        org="""---
+jupyter:
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+  extra:
+    key: value
+---
+""", target="""---
+jupyter:
+  extra:
+    key: value
+  jupytext:
+    notebook_metadata_filter: extra
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+"""):
+    nb = jupytext.reads(org, 'md')
+    text = jupytext.writes(nb, 'md')
+    compare(text, target)
+
+
+def test_update_metadata_filter_2(
+        no_jupytext_version_number,
+        org="""---
+jupyter:
+  jupytext:
+    notebook_metadata_filter: -extra
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+  extra:
+    key: value
+---
+""", target="""---
+jupyter:
+  jupytext:
+    notebook_metadata_filter: -extra
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+"""):
+    nb = jupytext.reads(org, 'md')
+    text = jupytext.writes(nb, 'md')
+    compare(text, target)