diff --git a/satpy/readers/li_base_nc.py b/satpy/readers/li_base_nc.py
index cefbcc7e55..1d1e56a850 100644
--- a/satpy/readers/li_base_nc.py
+++ b/satpy/readers/li_base_nc.py
@@ -439,11 +439,12 @@ def get_measured_variable(self, var_paths, fill_value=np.nan):
         # Also handle fill value here (but only if it is not None, so that we can still bypass this
         # step if needed)
         arr = self.apply_fill_value(arr, fill_value)
-
         return arr
 
     def apply_fill_value(self, arr, fill_value):
-        """Apply fill values, unless it is None."""
+        """Apply fill values, unless it is None and when _FillValue is provided."""
+        if arr.attrs.get("_FillValue") is None:
+            return arr
         if fill_value is not None:
             if np.isnan(fill_value):
                 fill_value = np.float32(np.nan)
diff --git a/satpy/tests/reader_tests/test_li_l2_nc.py b/satpy/tests/reader_tests/test_li_l2_nc.py
index 36cc930683..04f11acf4c 100644
--- a/satpy/tests/reader_tests/test_li_l2_nc.py
+++ b/satpy/tests/reader_tests/test_li_l2_nc.py
@@ -601,7 +601,6 @@ def test_coords_generation(self, filetype_infos):
         products = ["li_l2_af_nc",
                     "li_l2_afr_nc",
                     "li_l2_afa_nc"]
-
         for prod in products:
             handler = LIL2NCFileHandler("filename", {}, extract_filetype_info(filetype_infos, prod))
 
@@ -611,7 +610,6 @@ def test_coords_generation(self, filetype_infos):
 
             elevation = handler.get_measured_variable(handler.swath_coordinates["elevation"])
             elevation = handler.apply_use_rescaling(elevation)
-
             # Initialize proj_dict
             proj_var = handler.swath_coordinates["projection"]
             geos_proj = handler.get_measured_variable(proj_var, fill_value=None)
@@ -634,9 +632,6 @@ def test_coords_generation(self, filetype_infos):
             elevation_vals = elevation.values * point_height
             azimuth_vals *= -1
             lon_ref, lat_ref = projection(azimuth_vals, elevation_vals, inverse=True)
-            # Convert to float32:
-            lon_ref = lon_ref.astype(np.float32)
-            lat_ref = lat_ref.astype(np.float32)
 
             handler.generate_coords_from_scan_angles()
             lon = handler.internal_variables["longitude"].values