diff --git a/scripts/lib/CIME/case/case.py b/scripts/lib/CIME/case/case.py
index 2305bc4ccc6f..28c602dd1ba4 100644
--- a/scripts/lib/CIME/case/case.py
+++ b/scripts/lib/CIME/case/case.py
@@ -177,7 +177,10 @@ def initialize_derived_attributes(self):
         threads_per_core = 1 if (threads_per_node <= max_mpitasks_per_node) else smt_factor
         self.cores_per_task = self.thread_count / threads_per_core
 
-        os.environ["OMP_NUM_THREADS"] = str(self.thread_count)
+        if self.get_build_threaded():
+            os.environ["OMP_NUM_THREADS"] = str(self.thread_count)
+        elif "OMP_NUM_THREADS" in os.environ:
+            del os.environ["OMP_NUM_THREADS"]
 
         self.srun_binding = smt_factor*max_mpitasks_per_node / self.tasks_per_node
 
@@ -1417,7 +1420,10 @@ def load_env(self, reset=False, job=None, verbose=False):
         if not self._is_env_loaded or reset:
             if job is None:
                 job = self.get_primary_job()
-            os.environ["OMP_NUM_THREADS"] = str(self.thread_count)
+            if self.get_build_threaded():
+                os.environ["OMP_NUM_THREADS"] = str(self.thread_count)
+            elif "OMP_NUM_THREADS" in os.environ:
+                del os.environ["OMP_NUM_THREADS"]
             env_module = self.get_env("mach_specific")
             env_module.load_env(self, job=job, verbose=verbose)
             self._is_env_loaded = True
diff --git a/scripts/lib/CIME/case/case_run.py b/scripts/lib/CIME/case/case_run.py
index f7fc66a4a6bd..4495131eeaa1 100644
--- a/scripts/lib/CIME/case/case_run.py
+++ b/scripts/lib/CIME/case/case_run.py
@@ -76,7 +76,10 @@ def _run_model_impl(case, lid, skip_pnl=False, da_cycle=0):
     model = case.get_value("MODEL")
 
     # Set OMP_NUM_THREADS
-    os.environ["OMP_NUM_THREADS"] = str(case.thread_count)
+    if case.get_build_threaded():
+        os.environ["OMP_NUM_THREADS"] = str(case.thread_count)
+    elif "OMP_NUM_THREADS" in os.environ:
+        del os.environ["OMP_NUM_THREADS"]
 
     # Run the model
     cmd = case.get_mpirun_cmd(allow_unresolved_envvars=False)