diff --git a/docs/sphinx/source/whatsnew/v0.15.3.rst b/docs/sphinx/source/whatsnew/v0.15.3.rst
index b79b9aed66..7196127907 100644
--- a/docs/sphinx/source/whatsnew/v0.15.3.rst
+++ b/docs/sphinx/source/whatsnew/v0.15.3.rst
@@ -14,6 +14,12 @@ Deprecations
 
 Bug fixes
 ~~~~~~~~~
+~~~~~~~~
+
+* Fixed ``ModelChain`` no longer replacing missing (NaN) values in the DC
+  and AC results with zero. Genuine gaps in the input now propagate as NaN,
+  following the "NaN in, NaN out" policy, while nighttime correctly remains
+  zero power. (:issue:`1409`)
 
 
 Enhancements
diff --git a/pvlib/modelchain.py b/pvlib/modelchain.py
index 45374bd6fa..d417faeb01 100644
--- a/pvlib/modelchain.py
+++ b/pvlib/modelchain.py
@@ -665,7 +665,10 @@ def _make_diode_params(photocurrent, saturation_current,
             self.results.dc,
             unwrap=False
         )
-        self.results.dc = tuple(dc.fillna(0) for dc in self.results.dc)
+        # Missing (NaN) values in the inputs are intentionally preserved so
+        # that the result follows the "NaN in, NaN out" policy. At night the
+        # single diode model already returns zero power, so night is not
+        # affected by not filling NaNs here.
         # If the system has one Array, unwrap the single return value
         # to preserve the original behavior of ModelChain
         if self.system.num_arrays == 1:
@@ -766,7 +769,10 @@ def adr_inverter(self):
 
     def pvwatts_inverter(self):
         ac = self.system.get_ac('pvwatts', self.results.dc)
-        self.results.ac = ac.fillna(0)
+        # Missing (NaN) values in the DC input are preserved so that the
+        # result follows the "NaN in, NaN out" policy instead of silently
+        # reporting zero AC for missing data.
+        self.results.ac = ac
         return self
 
     @property
diff --git a/tests/test_modelchain.py b/tests/test_modelchain.py
index 9ea804f014..49ee8354a3 100644
--- a/tests/test_modelchain.py
+++ b/tests/test_modelchain.py
@@ -360,6 +360,42 @@ def test_run_model_with_irradiance(sapm_dc_snl_ac_system, location):
     assert_series_equal(ac, expected)
 
 
+def test_run_model_preserves_nan_inputs(cec_dc_snl_ac_system, location):
+    # regression test for gh-1409: genuine missing (NaN) values in the
+    # weather must not be silently replaced with zero in the DC results.
+    # Nighttime (zero irradiance) should still yield zero power.
+    mc = ModelChain(cec_dc_snl_ac_system, location, dc_model='cec')
+    times = pd.date_range('20160101 1200-0700', periods=3, freq='6h')
+    weather = pd.DataFrame(
+        {'ghi': [500, np.nan, 0], 'dni': [800, np.nan, 0],
+         'dhi': [100, np.nan, 0]},
+        index=times)
+    mc.run_model(weather)
+    dc = mc.results.dc
+    # a missing input is preserved as NaN ...
+    assert np.isnan(dc['p_mp'].iloc[1])
+    # ... while nighttime remains zero power, not NaN ...
+    assert dc['p_mp'].iloc[2] == pytest.approx(0)
+    # ... and the daytime value is a sensible positive number.
+    assert dc['p_mp'].iloc[0] > 0
+
+
+def test_pvwatts_inverter_preserves_nan_inputs(
+        pvwatts_dc_pvwatts_ac_system, location):
+    # regression test for gh-1409: the pvwatts inverter must not replace
+    # missing DC values with zero AC power.
+    mc = ModelChain(pvwatts_dc_pvwatts_ac_system, location,
+                    aoi_model='no_loss')
+    times = pd.date_range('20160101 1200-0700', periods=3, freq='6h')
+    weather = pd.DataFrame(
+        {'ghi': [500, np.nan, 0], 'dni': [800, np.nan, 0],
+         'dhi': [100, np.nan, 0]},
+        index=times)
+    ac = mc.run_model(weather).results.ac
+    assert np.isnan(ac.iloc[1])
+    assert ac.iloc[2] == pytest.approx(0)
+
+
 @pytest.fixture(scope='function')
 def multi_array_sapm_dc_snl_ac_system(
         sapm_temperature_cs5p_220m, sapm_module_params,