diff --git a/doc/whats-new.rst b/doc/whats-new.rst
index f17bb8f0d49..988e47511fa 100644
--- a/doc/whats-new.rst
+++ b/doc/whats-new.rst
@@ -126,6 +126,9 @@ Bug fixes
 - Compatibility fixes to plotting module for Numpy 1.14 and Pandas 0.22
   (:issue:`1813`).
   By `Joe Hamman <https://github.com/jhamman>`_.
+- Bug fix in encoding coordinates with ``{'_FillValue': None}`` in netCDF
+  metadata (:issue:`1865`).
+  By `Chris Roth <https://github.com/czr137>`_.
 - Fix indexing with lists for arrays loaded from netCDF files with
   ``engine='h5netcdf`` (:issue:`1864`).
   By `Stephan Hoyer <https://github.com/shoyer>`_.
diff --git a/xarray/backends/netCDF4_.py b/xarray/backends/netCDF4_.py
index b3cb1d8e49f..3f3364dec56 100644
--- a/xarray/backends/netCDF4_.py
+++ b/xarray/backends/netCDF4_.py
@@ -160,7 +160,7 @@ def _extract_nc4_variable_encoding(variable, raise_on_invalid=False,
 
     safe_to_drop = set(['source', 'original_shape'])
     valid_encodings = set(['zlib', 'complevel', 'fletcher32', 'contiguous',
-                           'chunksizes', 'shuffle'])
+                           'chunksizes', 'shuffle', '_FillValue'])
     if lsd_okay:
         valid_encodings.add('least_significant_digit')
 
diff --git a/xarray/backends/scipy_.py b/xarray/backends/scipy_.py
index dba2e5672a2..a608cff8eb5 100644
--- a/xarray/backends/scipy_.py
+++ b/xarray/backends/scipy_.py
@@ -188,8 +188,9 @@ def encode_variable(self, variable):
     def prepare_variable(self, name, variable, check_encoding=False,
                          unlimited_dims=None):
         if check_encoding and variable.encoding:
-            raise ValueError('unexpected encoding for scipy backend: %r'
-                             % list(variable.encoding))
+            if variable.encoding != {'_FillValue': None}:
+                raise ValueError('unexpected encoding for scipy backend: %r'
+                                 % list(variable.encoding))
 
         data = variable.data
         # nb. this still creates a numpy array in all memory, even though we
diff --git a/xarray/tests/test_backends.py b/xarray/tests/test_backends.py
index 85b6bdea346..e88fc790571 100644
--- a/xarray/tests/test_backends.py
+++ b/xarray/tests/test_backends.py
@@ -704,6 +704,26 @@ def test_explicitly_omit_fill_value(self):
         with self.roundtrip(ds) as actual:
             assert '_FillValue' not in actual.x.encoding
 
+    def test_explicitly_omit_fill_value_via_encoding_kwarg(self):
+        ds = Dataset({'x': ('y', [np.pi, -np.pi])})
+        kwargs = dict(encoding={'x': {'_FillValue': None}})
+        with self.roundtrip(ds, save_kwargs=kwargs) as actual:
+            assert '_FillValue' not in actual.x.encoding
+        self.assertEqual(ds.y.encoding, {})
+
+    def test_explicitly_omit_fill_value_in_coord(self):
+        ds = Dataset({'x': ('y', [np.pi, -np.pi])}, coords={'y': [0.0, 1.0]})
+        ds.y.encoding['_FillValue'] = None
+        with self.roundtrip(ds) as actual:
+            assert '_FillValue' not in actual.y.encoding
+
+    def test_explicitly_omit_fill_value_in_coord_via_encoding_kwarg(self):
+        ds = Dataset({'x': ('y', [np.pi, -np.pi])}, coords={'y': [0.0, 1.0]})
+        kwargs = dict(encoding={'y': {'_FillValue': None}})
+        with self.roundtrip(ds, save_kwargs=kwargs) as actual:
+            assert '_FillValue' not in actual.y.encoding
+        self.assertEqual(ds.y.encoding, {})
+
     def test_encoding_same_dtype(self):
         ds = Dataset({'x': ('y', np.arange(10.0, dtype='f4'))})
         kwargs = dict(encoding={'x': {'dtype': 'f4'}})