diff --git a/CHANGES.rst b/CHANGES.rst
index 4cbe4ea9eb..a28cf50218 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -9,6 +9,8 @@ Bug Fixes
 Cubeviz
 ^^^^^^^
 
+- Fixed multiple select handling for batch mode aperture photometry in Cubeviz. [#3163]
+
 Imviz
 ^^^^^
 
diff --git a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py
index a189d33254..c02e87c8b5 100644
--- a/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py
+++ b/jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.py
@@ -114,7 +114,8 @@ def valid_cubeviz_datasets(data):
                                     'photon flux density wav',
                                     'spectral flux density',
                                     'photon flux density',
-                                    'energy flux']  # Moment map 0
+                                    'energy flux',  # Moment map 0
+                                    'surface brightness']
                 return ((data.ndim in (2, 3)) and
                         ((img_unit == (u.MJy / u.sr)) or
                          (img_unit.physical_type in acceptable_types)))
@@ -143,10 +144,19 @@ def _on_dataset_selected_changed(self, event={}):
         if self.config != "cubeviz":
             return
         # self.dataset might not exist when app is setting itself up.
-        if hasattr(self, "dataset") and self.dataset.selected_dc_item.ndim > 2:
-            self.is_cube = True
-        else:
+        if hasattr(self, "dataset"):
+            if isinstance(self.dataset.selected_dc_item, list):
+                datasets = self.dataset.selected_dc_item
+            else:
+                datasets = [self.dataset.selected_dc_item]
+
             self.is_cube = False
+            for dataset in datasets:
+                # This assumes all cubes, or no cubes. If we allow photometry on collapsed cubes
+                # or images this will need to change.
+                if dataset.ndim > 2:
+                    self.is_cube = True
+                    break
 
     def _get_defaults_from_metadata(self, dataset=None):
         defaults = {}
@@ -842,6 +852,7 @@ def calculate_batch_photometry(self, options=[], add_to_table=True, update_plots
                 option.setdefault('pixel_area', defaults.get('pixel_area', 0))
             if self.flux_scaling_multi_auto:
                 option.setdefault('flux_scaling', defaults.get('flux_scaling', 0))
+
             try:
                 self.calculate_photometry(add_to_table=add_to_table,
                                           update_plots=this_update_plots,
diff --git a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py
index 262d5d65c7..4ebb683e54 100644
--- a/jdaviz/configs/imviz/tests/test_simple_aper_phot.py
+++ b/jdaviz/configs/imviz/tests/test_simple_aper_phot.py
@@ -489,3 +489,33 @@ def test_curve_of_growth(with_unit):
     with pytest.raises(TypeError, match='Unsupported aperture'):
         _curve_of_growth(data, cen, EllipticalAnnulus(cen, 3, 8, 5), 100,
                          pixarea_fac=pixarea_fac)
+
+
+def test_cubeviz_batch(cubeviz_helper, spectrum1d_cube_fluxunit_jy_per_steradian):
+    cubeviz_helper.load_data(spectrum1d_cube_fluxunit_jy_per_steradian, data_label='test')
+    phot_plugin = cubeviz_helper.plugins['Aperture Photometry']._obj
+    uc_plugin = cubeviz_helper.plugins['Unit Conversion']
+
+    cubeviz_helper.load_regions(CirclePixelRegion(center=PixCoord(x=5, y=5), radius=2))
+    cubeviz_helper.load_regions(CirclePixelRegion(center=PixCoord(x=3, y=3), radius=2))
+
+    phot_plugin.dataset_selected = 'test[FLUX]'
+    phot_plugin.multiselect = True
+    phot_plugin.aperture.selected = ['Subset 1', 'Subset 2']
+
+    phot_plugin.calculate_batch_photometry(full_exceptions=True)
+    assert len(phot_plugin.table) == 2
+    tbl = cubeviz_helper.get_aperture_photometry_results()
+    assert_quantity_allclose(tbl['sum'], [5.980836e-12, 2.037396e-10] * u.Jy, rtol=1e-4)
+
+    # Test that it still works after unit conversion
+    uc_plugin.flux_unit = 'MJy'
+
+    phot_plugin.calculate_batch_photometry(full_exceptions=True)
+
+    assert len(phot_plugin.table) == 4
+    tbl = cubeviz_helper.get_aperture_photometry_results()
+    # get_aperture_photometry_results converts all to the same units
+    assert_quantity_allclose(tbl['sum'],
+                             [5.980836e-12, 2.037396e-10, 5.980836e-12, 2.037396e-10] * u.Jy,
+                             rtol=1e-4)