diff --git a/.github/workflows/ubuntu-ci-x86_64-gnu.yaml b/.github/workflows/ubuntu-ci-x86_64-gnu.yaml
index 48b8bba49..a20b969dc 100644
--- a/.github/workflows/ubuntu-ci-x86_64-gnu.yaml
+++ b/.github/workflows/ubuntu-ci-x86_64-gnu.yaml
@@ -177,7 +177,7 @@ jobs:
 
           # Test environment chaining
           echo "Test environment chaining"
-          spack stack create env --name chaintest --template empty --site linux.default --upstream ${ENVDIR}/install --compiler gcc
+          spack stack create env --name chaintest --template empty --site linux.default --compiler gcc --upstream ${ENVDIR}/install
           # Retain config from upstream so we don't have to rebuild:
           cp -r ${ENVDIR}/{site,common} $PWD/envs/chaintest/.
           spack env activate ${PWD}/envs/chaintest
@@ -186,6 +186,12 @@ jobs:
           unwanted_duplicates=$(( cat envs/chaintest/log.concretize | grep -E '^ - ' | grep -Fv 'nccmp@1.9.0.1' || true ) | wc -l)
           if [ ${unwanted_duplicates} -gt 0 ]; then echo "Environment chaining test failed"; exit 1; fi
           spack env deactivate
+          echo "Verify 'create env' warnings"
+          echo "# nothing" >> ${SPACK_STACK_DIR}/envs/chaintest/site/packages.yaml
+          echo "# nothing" >> ${SPACK_STACK_DIR}/envs/chaintest/common/packages.yaml
+          spack stack create env --name chaintest3 --site linux.default --compiler gcc --upstream ${SPACK_STACK_DIR}/envs/chaintest/install 2>&1 | tee stderr.txt
+          cnt=$(grep -c "WARNING.*do not match" stderr.txt || true)
+          if [ $cnt -ne 2 ]; then echo "Missing 'create env' warnings"; exit 1; fi
 
       - name: test-env
         run: |
diff --git a/spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py b/spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py
index d4317fc4d..b63dd93f1 100644
--- a/spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py
+++ b/spack-ext/lib/jcsda-emc/spack-stack/stack/stack_env.py
@@ -1,5 +1,6 @@
 from collections import OrderedDict
 import copy
+import filecmp
 import io
 import logging
 import os
@@ -279,6 +280,10 @@ def write(self):
             spack.config.add(lmod_prefix, scope=env_scope)
             spack.config.add(tcl_prefix, scope=env_scope)
         if self.upstreams:
+            env_config_dirs = {
+                "common": os.path.join(self.env_dir(), "common"),
+                "site": os.path.join(self.env_dir(), "site"),
+            }
             for upstream_path in self.upstreams:
                 upstream_path = upstream_path[0]
                 # spack doesn't handle "~/" correctly, this fixes it:
@@ -301,6 +306,24 @@ def write(self):
                 upstream = "upstreams:%s:install_tree:'%s'" % (name, upstream_path)
                 logging.info("Adding upstream path '%s'" % upstream_path)
                 spack.config.add(upstream, scope=env_scope)
+                # Verify that config files match
+                upstream_config_dirs = {
+                    "common": os.path.normpath(os.path.join(upstream_path, "../common/")),
+                    "site": os.path.normpath(os.path.join(upstream_path, "../site/")),
+                }
+                for n in ("common", "site"):
+                    if not os.path.isdir(upstream_config_dirs[n]):
+                        does_not_match = True
+                    else:
+                        comparison = filecmp.dircmp(upstream_config_dirs[n], env_config_dirs[n])
+                        does_not_match = comparison.diff_files or comparison.left_only or comparison.right_only
+                    if does_not_match:
+                        logging.warning(
+                            (f"WARNING: {n} config directories for this environment and upstream "
+                             f"'{upstream_path}' do not match! Verify that you are using the same "
+                              "version of spack-stack, or really, really know what you are doing.")
+                        )
+
         if self.modifypkg:
             logging.info("Creating custom repo with packages %s" % ", ".join(self.modifypkg))
             env_repo_path = os.path.join(env_dir, "envrepo")