diff --git a/jupytext/jupytext.py b/jupytext/jupytext.py
index 54a501712..bb51ce565 100644
--- a/jupytext/jupytext.py
+++ b/jupytext/jupytext.py
@@ -13,7 +13,7 @@
 import io
 from copy import deepcopy
 from nbformat.v4.rwbase import NotebookReader, NotebookWriter
-from nbformat.v4.nbbase import new_notebook
+from nbformat.v4.nbbase import new_notebook, new_code_cell
 import nbformat
 from .formats import get_format, guess_format, \
     update_jupytext_formats_metadata, format_name_for_ext
@@ -43,6 +43,10 @@ def reads(self, s, **_):
 
         lines = lines[pos:]
 
+        if self.format.format_name and \
+                self.format.format_name.startswith('sphinx'):
+            cells.append(new_code_cell(source='%matplotlib inline'))
+
         while lines:
             reader = self.format.cell_reader_class(self.format.extension)
             cell, pos = reader.read(lines)
@@ -89,6 +93,11 @@ def writes(self, nb, **kwargs):
             text = cell.simplify_code_markers(
                 texts[i], texts[i + 1] if i + 1 < len(texts) else None, lines)
 
+            if i == 0 and self.format.format_name and \
+                    self.format.format_name.startswith('sphinx') and \
+                    text == ['%matplotlib inline']:
+                continue
+
             lines.extend(text)
             lines.extend([''] * cell.lines_to_next_cell)
 
diff --git a/tests/notebooks/mirror/sphinx-rst2md_to_ipynb/plot_notebook.ipynb b/tests/notebooks/mirror/sphinx-rst2md_to_ipynb/plot_notebook.ipynb
index d2fff2e8b..9cd3ae6b4 100644
--- a/tests/notebooks/mirror/sphinx-rst2md_to_ipynb/plot_notebook.ipynb
+++ b/tests/notebooks/mirror/sphinx-rst2md_to_ipynb/plot_notebook.ipynb
@@ -1,5 +1,14 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
diff --git a/tests/notebooks/mirror/sphinx_to_ipynb/plot_notebook.ipynb b/tests/notebooks/mirror/sphinx_to_ipynb/plot_notebook.ipynb
index 750672551..957774cfa 100644
--- a/tests/notebooks/mirror/sphinx_to_ipynb/plot_notebook.ipynb
+++ b/tests/notebooks/mirror/sphinx_to_ipynb/plot_notebook.ipynb
@@ -1,5 +1,14 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
diff --git a/tests/test_read_simple_sphinx.py b/tests/test_read_simple_sphinx.py
index 451ce302b..114860238 100644
--- a/tests/test_read_simple_sphinx.py
+++ b/tests/test_read_simple_sphinx.py
@@ -25,27 +25,30 @@ def f(x):
    return 4
 """):
     nb = jupytext.reads(script, ext='.py', format_name='sphinx')
-    assert nb.cells[0].cell_type == 'markdown'
-    assert nb.cells[0].source == 'This is a markdown cell'
+    assert nb.cells[0].cell_type == 'code'
+    assert nb.cells[0].source == '%matplotlib inline'
 
-    assert nb.cells[1].cell_type == 'code'
-    compare(nb.cells[1].source, '''1 + 2 + 3 + 4
+    assert nb.cells[1].cell_type == 'markdown'
+    assert nb.cells[1].source == 'This is a markdown cell'
+
+    assert nb.cells[2].cell_type == 'code'
+    compare(nb.cells[2].source, '''1 + 2 + 3 + 4
 5
 6''')
-    assert nb.cells[2].cell_type == 'markdown'
-    assert nb.cells[2].source == ''
+    assert nb.cells[3].cell_type == 'markdown'
+    assert nb.cells[3].source == ''
 
-    assert nb.cells[3].cell_type == 'code'
-    assert nb.cells[3].source == '7'
+    assert nb.cells[4].cell_type == 'code'
+    assert nb.cells[4].source == '7'
 
-    assert nb.cells[4].cell_type == 'markdown'
-    assert nb.cells[4].source == 'Another markdown cell'
+    assert nb.cells[5].cell_type == 'markdown'
+    assert nb.cells[5].source == 'Another markdown cell'
 
-    assert nb.cells[5].cell_type == 'code'
-    assert nb.cells[5].source == """def f(x):
+    assert nb.cells[6].cell_type == 'code'
+    assert nb.cells[6].source == """def f(x):
    '''Sample docstring'''
    return 4"""
-    assert len(nb.cells) == 6
+    assert len(nb.cells) == 7
 
     script2 = jupytext.writes(nb, ext='.py', format_name='sphinx')
     compare(script, script2)
@@ -71,26 +74,29 @@ def test_read_more_complex_file(script="""'''This is a markdown cell'''
 """):
     nb = jupytext.reads(script, ext='.py', format_name='sphinx')
 
-    assert nb.cells[0].cell_type == 'markdown'
-    assert nb.cells[0].source == 'This is a markdown cell'
+    assert nb.cells[0].cell_type == 'code'
+    assert nb.cells[0].source == '%matplotlib inline'
 
-    assert nb.cells[1].cell_type == 'code'
-    compare(nb.cells[1].source, '''1 + 2 + 3 + 4
+    assert nb.cells[1].cell_type == 'markdown'
+    assert nb.cells[1].source == 'This is a markdown cell'
+
+    assert nb.cells[2].cell_type == 'code'
+    compare(nb.cells[2].source, '''1 + 2 + 3 + 4
 5
 6''')
-    assert nb.cells[2].cell_type == 'markdown'
-    assert nb.cells[2].source == 'Another markdown cell'
-
     assert nb.cells[3].cell_type == 'markdown'
-    assert nb.cells[3].source == 'A third one'
+    assert nb.cells[3].source == 'Another markdown cell'
 
     assert nb.cells[4].cell_type == 'markdown'
-    assert nb.cells[4].source == 'Another markdown cell'
+    assert nb.cells[4].source == 'A third one'
 
-    assert nb.cells[5].cell_type == 'code'
-    assert nb.cells[5].source == '1 + 2 + 3 + 4'
+    assert nb.cells[5].cell_type == 'markdown'
+    assert nb.cells[5].source == 'Another markdown cell'
 
-    assert nb.cells[6].cell_type == 'markdown'
-    assert nb.cells[6].source == 'And a last one'
+    assert nb.cells[6].cell_type == 'code'
+    assert nb.cells[6].source == '1 + 2 + 3 + 4'
 
-    assert len(nb.cells) == 7
+    assert nb.cells[7].cell_type == 'markdown'
+    assert nb.cells[7].source == 'And a last one'
+
+    assert len(nb.cells) == 8