diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py b/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
index 89d0aa16dc..43e5cdf149 100644
--- a/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
+++ b/jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py
@@ -315,6 +315,16 @@ def uncert_cube(self):
     def spectral_display_unit(self):
         return astropy.units.Unit(self.app._get_display_unit(self.slice_display_unit_name))
 
+    @property
+    def mask_non_science(self):
+        # Aperture masks begin by finding removing from consideration any pixel
+        # set to NaN, which corresponds to a pixel on the "non-science" portions
+        # of the detector. For JWST spectral cubes, these pixels are marked in
+        # the DQ array with flag `513`.
+        return np.logical_not(
+            np.isnan(self.dataset.selected_obj.flux.value)
+        ).astype(float)
+
     @property
     def aperture_weight_mask(self):
         # Exact slice mask of cone or cylindrical aperture through the cube. `weight_mask` is
@@ -322,21 +332,31 @@ def aperture_weight_mask(self):
         # wavelength, on the range [0, 1].
         if self.aperture.selected == self.aperture.default_text:
             # Entire Cube
-            return np.ones_like(self.dataset.selected_obj.flux.value)
-        return self.aperture.get_mask(self.dataset.selected_obj,
-                                      self.aperture_method_selected,
-                                      self.spectral_display_unit,
-                                      self.reference_spectral_value if self.wavelength_dependent else None)  # noqa
+            return self.mask_non_science
+
+        return (
+            self.mask_non_science *
+            self.aperture.get_mask(
+                self.dataset.selected_obj,
+                self.aperture_method_selected,
+                self.spectral_display_unit,
+                self.reference_spectral_value if self.wavelength_dependent else None)
+        )
 
     @property
     def bg_weight_mask(self):
         if self.background.selected == self.background.default_text:
             # NO background
             return np.zeros_like(self.dataset.selected_obj.flux.value)
-        return self.background.get_mask(self.dataset.selected_obj,
-                                        self.aperture_method_selected,
-                                        self.spectral_display_unit,
-                                        self.reference_spectral_value if self.bg_wavelength_dependent else None)  # noqa
+
+        return (
+            self.mask_non_science *
+            self.background.get_mask(
+                self.dataset.selected_obj,
+                self.aperture_method_selected,
+                self.spectral_display_unit,
+                self.reference_spectral_value if self.bg_wavelength_dependent else None)
+        )
 
     @property
     def aperture_area_along_spectral(self):
diff --git a/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py b/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
index 56bdc9902d..9e8e643ffa 100644
--- a/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
+++ b/jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
@@ -5,6 +5,7 @@
 import numpy as np
 from astropy import units as u
 from astropy.nddata import NDDataArray, StdDevUncertainty
+from astropy.tests.helper import assert_quantity_allclose
 from astropy.utils.exceptions import AstropyUserWarning
 from glue.core.roi import CircularROI, RectangularROI
 from glue.core.edit_subset_mode import ReplaceMode, AndNotMode, NewMode
@@ -518,3 +519,26 @@ def test_spectral_extraction_with_correct_sum_units(cubeviz_helper,
     )
     assert collapsed.flux.unit == u.Jy
     assert collapsed.uncertainty.unit == u.Jy
+
+
+def test_default_spectral_extraction(cubeviz_helper, spectrum1d_cube_fluxunit_jy_per_steradian):
+    # spacetelescope/jdaviz#3086 reported that the default cube
+    # spectral extraction in cubeviz did not match the spectral extraction
+    # for a spatial subset that captures all spaxels. this regression tests
+    # make sure that doesn't happen anymore by accounting for non-science pixels
+    # in the sums:
+    cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian)
+    flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
+
+    # create a spatial subset that spans all spaxels:
+    flux_viewer.apply_roi(CircularROI(1.5, 2, 5))
+
+    # the first and second spectra correspond to the default extraction
+    # and the subset extraction. the fluxes in these extractions should agree:
+    extracted_spectra = list(
+        cubeviz_helper.specviz.get_spectra(apply_slider_redshift=False).values()
+    )
+
+    assert_quantity_allclose(
+        extracted_spectra[0].flux, extracted_spectra[1].flux
+    )