diff --git a/jupytext/cell_to_text.py b/jupytext/cell_to_text.py
index 47a572951..a39a3dc3d 100644
--- a/jupytext/cell_to_text.py
+++ b/jupytext/cell_to_text.py
@@ -115,6 +115,7 @@ def __init__(self, *args, **kwargs):
         self.comment = ''
 
     def html_comment(self, metadata, code='region'):
+        """Protect a Markdown or Raw cell with HTML comments"""
         if metadata:
             region_start = ['<!-- #' + code]
             if 'title' in metadata and '{' not in metadata['title']:
@@ -143,17 +144,17 @@ def code_to_text(self):
         comment_magic(source, self.language, self.comment_magics)
 
         options = []
+        self.language = self.metadata.pop('language', self.language)
         if self.cell_type == 'code' and self.language:
             options.append(self.language)
 
-        filtered_metadata = {key: self.metadata[key] for key in self.metadata
-                             if key not in ['active', 'language']}
-
-        if filtered_metadata:
-            options.append(metadata_to_md_options(filtered_metadata))
+        if self.metadata:
+            options.append(metadata_to_md_options(self.metadata))
 
         if self.cell_type == 'raw':
-            return self.html_comment(filtered_metadata, 'raw')
+            if self.metadata.get('active') == '':
+                self.metadata.pop('active')
+            return self.html_comment(self.metadata, 'raw')
 
         return ['```{}'.format(' '.join(options))] + source + ['```']
 
diff --git a/tests/test_active_cells.py b/tests/test_active_cells.py
index 71e956ebb..ee11da1f2 100644
--- a/tests/test_active_cells.py
+++ b/tests/test_active_cells.py
@@ -17,7 +17,13 @@
 # ---
 
 ''',
+          '.md': '''---
+jupyter:
+  jupytext:
+    main_language: python
+---
 
+''',
           '.Rmd': '''---
 jupyter:
   jupytext:
@@ -32,6 +38,10 @@
               '.Rmd': """```{python active="ipynb,py,R,Rmd"}
 # This cell is active in all extensions
 ```
+""",
+              '.md': """```python active="ipynb,py,R,Rmd"
+# This cell is active in all extensions
+```
 """,
               '.R': """# + {"active": "ipynb,py,R,Rmd"}
 # This cell is active in all extensions
@@ -43,7 +53,7 @@
                          'outputs': []}}
 
 
-@pytest.mark.parametrize('ext', ['.Rmd', '.py', '.R'])
+@pytest.mark.parametrize('ext', ['.Rmd', '.md', '.py', '.R'])
 def test_active_all(ext, no_jupytext_version_number):
     nb = jupytext.reads(HEADER[ext] + ACTIVE_ALL[ext], ext)
     assert len(nb.cells) == 1
@@ -59,6 +69,11 @@ def test_active_all(ext, no_jupytext_version_number):
 # This cell is active only in ipynb
 %matplotlib inline
 ```
+""",
+                '.md': """```python active="ipynb"
+# This cell is active only in ipynb
+%matplotlib inline
+```
 """,
                 '.R': """# + {"active": "ipynb"}
 # # This cell is active only in ipynb
@@ -73,7 +88,7 @@ def test_active_all(ext, no_jupytext_version_number):
 
 
 @skip_if_dict_is_not_ordered
-@pytest.mark.parametrize('ext', ['.Rmd', '.py', '.R'])
+@pytest.mark.parametrize('ext', ['.Rmd', '.md', '.py', '.R'])
 def test_active_ipynb(ext, no_jupytext_version_number):
     nb = jupytext.reads(HEADER[ext] + ACTIVE_IPYNB[ext], ext)
     assert len(nb.cells) == 1
@@ -89,6 +104,11 @@ def test_active_ipynb(ext, no_jupytext_version_number):
 # This cell is active only in ipynb and Rmd
 # %matplotlib inline
 ```
+""",
+                              '.md': """```python tags=["active-ipynb-Rmd"]
+# This cell is active only in ipynb and Rmd
+%matplotlib inline
+```
 """,
                               '.R': """# + {"tags": ["active-ipynb-Rmd"]}
 # # This cell is active only in ipynb and Rmd
@@ -103,7 +123,7 @@ def test_active_ipynb(ext, no_jupytext_version_number):
 
 
 @skip_if_dict_is_not_ordered
-@pytest.mark.parametrize('ext', ['.Rmd', '.py', '.R'])
+@pytest.mark.parametrize('ext', ['.Rmd', '.md', '.py', '.R'])
 def test_active_ipynb_rmd_using_tags(ext, no_jupytext_version_number):
     nb = jupytext.reads(HEADER[ext] + ACTIVE_IPYNB_RMD_USING_TAG[ext], ext)
     assert len(nb.cells) == 1
@@ -137,6 +157,10 @@ def test_active_ipynb_rspin(no_jupytext_version_number):
                    '.Rmd': """```{python active="ipynb,py", eval=FALSE}
 # This cell is active in py and ipynb extensions
 ```
+""",
+                   '.md': """```python active="ipynb,py"
+# This cell is active in py and ipynb extensions
+```
 """,
                    '.R': """# + {"active": "ipynb,py"}
 # # This cell is active in py and ipynb extensions
@@ -150,7 +174,7 @@ def test_active_ipynb_rspin(no_jupytext_version_number):
 
 
 @skip_if_dict_is_not_ordered
-@pytest.mark.parametrize('ext', ['.Rmd', '.py', '.R'])
+@pytest.mark.parametrize('ext', ['.Rmd', '.md', '.py', '.R'])
 def test_active_py_ipynb(ext, no_jupytext_version_number):
     nb = jupytext.reads(HEADER[ext] + ACTIVE_PY_IPYNB[ext], ext)
     assert len(nb.cells) == 1