diff --git a/ipython_notebook_config.txt b/ipython_notebook_config.txt
index a961679..8646c94 100644
--- a/ipython_notebook_config.txt
+++ b/ipython_notebook_config.txt
@@ -81,7 +81,12 @@ def write_notebook_data_to_py(notebook_data, out_file_path):
                 output.write('\n')
                 for item in cell['source']:
                     if cell['cell_type']=='code':
-                        output.write(item)
+                        # Comment out ipython magic commands like "%matplotlib inline"
+                        if item[0] == '%':
+                            output.write('# ')
+                            output.write(item)
+                        else:
+                            output.write(item)
                     else:
                         output.write('# ')
                         output.write(item)
diff --git a/notebook_v4_to_py.py b/notebook_v4_to_py.py
index ec26c6d..2d07ab5 100644
--- a/notebook_v4_to_py.py
+++ b/notebook_v4_to_py.py
@@ -87,7 +87,12 @@ def write_notebook_data_to_py(notebook_data, out_file_path):
                 output.write('\n')
                 for item in cell['source']:
                     if cell['cell_type']=='code':
-                        output.write(item)
+                        # Comment out ipython magic commands like "%matplotlib inline"
+                        if item[0] == '%':
+                            output.write('# ')
+                            output.write(item)
+                        else:
+                            output.write(item)
                     else:
                         output.write('# ')
                         output.write(item)
diff --git a/py_to_notebook_v4.py b/py_to_notebook_v4.py
index 399ac23..4c97b84 100644
--- a/py_to_notebook_v4.py
+++ b/py_to_notebook_v4.py
@@ -112,7 +112,11 @@ def open_cell(line, execution_count):
             else:
                 source.append(line)
         elif current_cell=='code':
-            source.append(line)
+            # Remove comments for ipython magic commands like "%matplotlib inline"
+            if line[0:3] == '# %':
+                source.append(line[2:])
+            else:
+                source.append(line)
 
     last_cell = True
     outputcells = close_cell(current_cell)