diff --git a/aviary/core/aviary_group.py b/aviary/core/aviary_group.py
index 69f19ca32..21e3263dc 100644
--- a/aviary/core/aviary_group.py
+++ b/aviary/core/aviary_group.py
@@ -106,6 +106,23 @@ def configure(self):
             # Under MPI, promotion info only lives on rank 0, so broadcast.
             all_prom_inputs = self.comm.bcast(all_prom_inputs, root=0)
 
+        # Find all variables that are shape_by_conn so we don't set their shape with a stale value
+        # from the default metadata. We can only find these on the next level down because
+        # aviary_group's setup is not complete until after configure.
+        sbc_vars = []
+        for sub in self.system_iter(recurse=False, typ=om.Group):
+            pr2abs = sub._resolver.prom2abs_iter('input')
+            sub_inputs = [
+                (k, v[0]) for k, v in pr2abs if k.startswith('aircraft') or k.startswith('mission')
+            ]
+            abs2meta = sub._var_abs2meta['input']
+
+            for data in sub_inputs:
+                prom_name, abs_name = data
+                meta = abs2meta[abs_name]
+                if meta.get('shape_by_conn') is True:
+                    sbc_vars.append(prom_name)
+
         for key in aviary_metadata:
             if ':' not in key or key.startswith('dynamic:'):
                 continue
@@ -127,7 +144,12 @@ def configure(self):
                     # optional, but no default value
                     continue
 
-            self.set_input_defaults(key, val=val, units=units)
+            kwargs = {'units': units}
+            if key not in sbc_vars:
+                # Default val if var doesn't use shape_by_conn.
+                kwargs['val'] = val
+
+            self.set_input_defaults(key, **kwargs)
 
         # try to get all the possible EOMs from the Enums rather than specifically calling the names here
         # This will require some modifications to the enums
diff --git a/aviary/interface/test/test_shape_by_conn.py b/aviary/interface/test/test_shape_by_conn.py
new file mode 100644
index 000000000..cc26478aa
--- /dev/null
+++ b/aviary/interface/test/test_shape_by_conn.py
@@ -0,0 +1,103 @@
+from copy import deepcopy
+import unittest
+
+import numpy as np
+import openmdao.api as om
+from openmdao.utils.testing_utils import use_tempdirs
+
+from aviary.core.aviary_problem import AviaryProblem
+from aviary.utils.develop_metadata import add_meta_data
+from aviary.models.external_subsystems.detailed_battery.battery_variables import Aircraft, Dynamic
+from aviary.models.missions.energy_state_default import phase_info as energy_phase_info
+from aviary.subsystems.subsystem_builder import SubsystemBuilder
+from aviary.variable_info.variable_meta_data import CoreMetaData
+from aviary.variable_info.variables import Aircraft
+
+
+@use_tempdirs
+class TestShapebyConn(unittest.TestCase):
+    def test_shape_bug(self):
+        # Verifies that shape_by_conn variables no longer raise an exception during
+        # setup.
+
+        class ExtendedAircraft(Aircraft):
+            """Aircraft data hierarchy with one new var."""
+
+            class Wing(Aircraft.Wing):
+                CG1 = 'aircraft:wing:cg1'
+                CG2 = 'aircraft:wing:cg2'
+
+        ExtendedMetaData = CoreMetaData
+        add_meta_data(
+            ExtendedAircraft.Wing.CG1,
+            units='ft',
+            desc='CG of the wing.',
+            default_value=1.0,
+            meta_data=CoreMetaData,
+        )
+
+        add_meta_data(
+            ExtendedAircraft.Wing.CG2,
+            units='ft',
+            desc='CG of the wing.',
+            default_value=1.0,
+            meta_data=CoreMetaData,
+        )
+
+        class SBC(om.ExplicitComponent):
+            """This component has an input with shape_by_conn."""
+
+            def setup(self):
+                self.add_input(ExtendedAircraft.Wing.CG1, units='ft', shape_by_conn=True)
+                self.add_input('cg_promote_me', units='ft', shape_by_conn=True)
+
+                self.add_output('stuff', units='ft**2', copy_shape=ExtendedAircraft.Wing.CG1)
+
+            def compute(self, inputs, outputs):
+                pass
+
+        class CGBuilder(SubsystemBuilder):
+            _default_name = 'cg_sub'
+
+            def build_post_mission(
+                self,
+                aviary_inputs=None,
+                mission_info=None,
+                subsystem_options=None,
+                phase_mission_bus_lengths=None,
+            ):
+                grp = om.Group()
+                grp.add_subsystem(
+                    'sbc',
+                    SBC(),
+                    promotes_inputs=[
+                        ExtendedAircraft.Wing.CG1,
+                        ('cg_promote_me', ExtendedAircraft.Wing.CG2),
+                    ],
+                )
+                return grp
+
+        local_phase_info = deepcopy(energy_phase_info)
+
+        prob = AviaryProblem(meta_data=ExtendedMetaData)
+
+        prob.load_inputs(
+            'subsystems/aerodynamics/flops_based/test/data/high_wing_single_aisle.csv',
+            local_phase_info,
+        )
+        prob.load_external_subsystems([CGBuilder()])
+        # Preprocess inputs
+        prob.check_and_preprocess_inputs()
+
+        prob.build_model()
+
+        prob.setup()
+
+        prob.set_val(ExtendedAircraft.Wing.CG1, np.ones((3, 4)))
+        prob.set_val(ExtendedAircraft.Wing.CG2, np.ones((4, 2)))
+
+        prob.final_setup()
+
+
+if __name__ == '__main__':
+    unittest.main()