diff --git a/acceptance/bundle/override/job_cluster_var/databricks.yml b/acceptance/bundle/override/job_cluster_var/databricks.yml
index 546cc2d8a..48e68c926 100644
--- a/acceptance/bundle/override/job_cluster_var/databricks.yml
+++ b/acceptance/bundle/override/job_cluster_var/databricks.yml
@@ -20,7 +20,6 @@ targets:
       jobs:
         foo:
           job_clusters:
-            # This does not work because merging is done before resolution
             - job_cluster_key: "${var.mykey}"
               new_cluster:
                 node_type_id: i3.xlarge
diff --git a/acceptance/bundle/override/job_cluster_var/output.txt b/acceptance/bundle/override/job_cluster_var/output.txt
index dee2a3b5b..cb76de5a8 100644
--- a/acceptance/bundle/override/job_cluster_var/output.txt
+++ b/acceptance/bundle/override/job_cluster_var/output.txt
@@ -9,17 +9,12 @@
     "edit_mode": "UI_LOCKED",
     "format": "MULTI_TASK",
     "job_clusters": [
-      {
-        "job_cluster_key": "key",
-        "new_cluster": {
-          "spark_version": "13.3.x-scala2.12"
-        }
-      },
       {
         "job_cluster_key": "key",
         "new_cluster": {
           "node_type_id": "i3.xlarge",
-          "num_workers": 1
+          "num_workers": 1,
+          "spark_version": "13.3.x-scala2.12"
         }
       }
     ],
@@ -51,17 +46,12 @@ Validation OK!
     "edit_mode": "UI_LOCKED",
     "format": "MULTI_TASK",
     "job_clusters": [
-      {
-        "job_cluster_key": "key",
-        "new_cluster": {
-          "spark_version": "13.3.x-scala2.12"
-        }
-      },
       {
         "job_cluster_key": "key",
         "new_cluster": {
           "node_type_id": "i3.2xlarge",
-          "num_workers": 4
+          "num_workers": 4,
+          "spark_version": "13.3.x-scala2.12"
         }
       }
     ],
diff --git a/bundle/phases/initialize.go b/bundle/phases/initialize.go
index f7b3cd608..913685bcf 100644
--- a/bundle/phases/initialize.go
+++ b/bundle/phases/initialize.go
@@ -33,10 +33,6 @@ func Initialize() bundle.Mutator {
 			// If it is an ancestor, this updates all paths to be relative to the sync root path.
 			mutator.SyncInferRoot(),
 
-			mutator.MergeJobClusters(),
-			mutator.MergeJobParameters(),
-			mutator.MergeJobTasks(),
-			mutator.MergePipelineClusters(),
 			mutator.InitializeWorkspaceClient(),
 			mutator.PopulateCurrentUser(),
 			mutator.LoadGitDetails(),
@@ -70,6 +66,12 @@ func Initialize() bundle.Mutator {
 				"workspace",
 				"variables",
 			),
+
+			mutator.MergeJobClusters(),
+			mutator.MergeJobParameters(),
+			mutator.MergeJobTasks(),
+			mutator.MergePipelineClusters(),
+
 			// Provide permission config errors & warnings after initializing all variables
 			permissions.PermissionDiagnostics(),
 			mutator.SetRunAs(),