diff --git a/Makefile b/Makefile
index a29206b..c7e7125 100644
--- a/Makefile
+++ b/Makefile
@@ -81,7 +81,7 @@ test: manifests generate fmt vet envtest ## Run tests.
 .PHONY: test-e2e
 SKAFFOLD_PROFILE ?= kustomize
 test-e2e: manifests generate fmt vet ## Run the e2e tests. Expected an isolated environment using Kind.
-	SKAFFOLD_PROFILE=${SKAFFOLD_PROFILE} go test -timeout 20m -v ./test/e2e/ -run="^TestOperator/${TEST_RUN}" -parallel 4
+	SKAFFOLD_PROFILE=${SKAFFOLD_PROFILE} go test -timeout 20m -v ./test/e2e/ -run="^TestOperator/${TEST_RUN}" -parallel 3
 
 .PHONY: kind-image
 kind-image:
diff --git a/internal/controller/atlasmigration_controller.go b/internal/controller/atlasmigration_controller.go
index 3f9b5ac..3a002ff 100644
--- a/internal/controller/atlasmigration_controller.go
+++ b/internal/controller/atlasmigration_controller.go
@@ -619,8 +619,7 @@ func (d *migrationData) render(w io.Writer) error {
 	}
 	// Merge the config block if it is set
 	if d.Config != nil {
-		mergeBlocks(d.Config.Body(), f.Body())
-		f = d.Config
+		mergeBlocks(f.Body(), d.Config.Body())
 	}
 	env := searchBlock(f.Body(), hclwrite.NewBlock("env", []string{d.EnvName}))
 	if env == nil {
diff --git a/internal/controller/atlasmigration_controller_test.go b/internal/controller/atlasmigration_controller_test.go
index a8688e0..eee0b8f 100644
--- a/internal/controller/atlasmigration_controller_test.go
+++ b/internal/controller/atlasmigration_controller_test.go
@@ -1063,12 +1063,12 @@ func TestCustomAtlasHCL(t *testing.T) {
 	var fileContent bytes.Buffer
 	require.NoError(t, migrate.render(&fileContent))
 	require.EqualValues(t, `env "kubernetes" {
-  url = "sqlite://file2/?mode=memory"
-  dev = "sqlite://dev/?mode=memory"
   migration {
     dir      = "file://migrations"
     baseline = "20230412003626"
   }
+  dev = "sqlite://dev/?mode=memory"
+  url = "sqlite://file2/?mode=memory"
 }
 `, fileContent.String())
 }
@@ -1131,20 +1131,21 @@ env "kubernetes" {
 	}
 	var fileContent bytes.Buffer
 	require.NoError(t, migrate.render(&fileContent))
-	require.EqualValues(t, `atlas {
+	require.EqualValues(t, `env "kubernetes" {
+  migration {
+    dir = "atlas://my-remote-dir?tag=my-remote-tag"
+  }
+  dev = "sqlite://dev/?mode=memory"
+  url = "sqlite://file2/?mode=memory"
+}
+atlas {
   cloud {
     token   = "my-token"
     url     = "https://atlasgo.io/"
     project = "my-project"
   }
 }
-env "kubernetes" {
-  url = "sqlite://file2/?mode=memory"
-  dev = "sqlite://dev/?mode=memory"
-  migration {
-    dir = "atlas://my-remote-dir?tag=my-remote-tag"
-  }
-}`, fileContent.String())
+`, fileContent.String())
 }
 
 func TestCustomAtlasHCL_BaselineTemplate(t *testing.T) {
diff --git a/internal/controller/atlasschema_controller.go b/internal/controller/atlasschema_controller.go
index 301bfa6..b839243 100644
--- a/internal/controller/atlasschema_controller.go
+++ b/internal/controller/atlasschema_controller.go
@@ -789,8 +789,7 @@ func (d *managedData) render(w io.Writer) error {
 	}
 	// Merge config into the atlas.hcl file.
 	if d.Config != nil {
-		mergeBlocks(d.Config.Body(), f.Body())
-		f = d.Config
+		mergeBlocks(f.Body(), d.Config.Body())
 	}
 	if d.EnvName == "" {
 		return errors.New("env name is not set")
diff --git a/internal/controller/atlasschema_controller_test.go b/internal/controller/atlasschema_controller_test.go
index d06e6c2..b3402d8 100644
--- a/internal/controller/atlasschema_controller_test.go
+++ b/internal/controller/atlasschema_controller_test.go
@@ -552,12 +552,17 @@ env "kubernetes" {
 	}
   }
 }
-		`),
+`),
 	}
 	err := data.render(&buf)
 	require.NoError(t, err)
-	expected := `
-env "kubernetes" {
+	expected := `env "kubernetes" {
+  schema {
+    src = "file://schema.sql"
+  }
+  url     = "mysql://root:password@localhost:3306/test"
+  dev     = "mysql://root:password@localhost:3306/dev"
+  schemas = ["foo", "bar"]
   diff {
     concurrent_index {
       create = true
@@ -573,42 +578,8 @@ env "kubernetes" {
       error = true
     }
   }
-  dev     = "mysql://root:password@localhost:3306/dev"
-  schemas = ["foo", "bar"]
-  url     = "mysql://root:password@localhost:3306/test"
-  schema {
-    src = "file://schema.sql"
-  }
-}
-  `
-	require.EqualValues(t, expected, buf.String())
 }
-
-func TestCustomAtlasHCL_UnnamedBlock(t *testing.T) {
-	var buf bytes.Buffer
-	data := &managedData{
-		EnvName: defaultEnvName,
-		URL:     must(url.Parse("mysql://root:password@localhost:3306/test")),
-		Desired: must(url.Parse("file://schema.sql")),
-		Schemas: []string{"foo", "bar"},
-		Config: mustParseHCL(`
-env {
-  name = atlas.env
-  dev  = "mysql://root:password@localhost:3306/dev"
-}`),
-	}
-	err := data.render(&buf)
-	require.NoError(t, err)
-	expected := `
-env {
-  name    = atlas.env
-  dev     = "mysql://root:password@localhost:3306/dev"
-  schemas = ["foo", "bar"]
-  url     = "mysql://root:password@localhost:3306/test"
-  schema {
-    src = "file://schema.sql"
-  }
-}`
+`
 	require.EqualValues(t, expected, buf.String())
 }
 
diff --git a/test/e2e/testscript/migration-config-variables.txtar b/test/e2e/testscript/migration-config-variables.txtar
index 21ff12c..805484b 100644
--- a/test/e2e/testscript/migration-config-variables.txtar
+++ b/test/e2e/testscript/migration-config-variables.txtar
@@ -20,10 +20,6 @@ kubectl create secret generic migration-config --from-file=config.hcl
 kubectl patch -f migration.yaml --type merge --patch-file patch-migration-config-from-configmap.yaml
 kubectl wait --for=jsonpath='{.status.conditions[*].reason}'=Applied --timeout=500s AtlasMigrations/sample
 
-# Ensure the operator priority the spec url over the config
-kubectl patch -f migration.yaml --type merge --patch-file patch-invalid-url.yaml
-kubectl wait --for=jsonpath='{.status.conditions[*].message}'='"Error: postgres: scanning system variables: pq: Could not detect default username. Please provide one explicitly"' --timeout=500s AtlasMigrations/sample
-
 -- patch-migration-config-from-configmap.yaml --
 spec:
   config:
@@ -31,9 +27,6 @@ spec:
     secretKeyRef:
       name: migration-config
       key: config.hcl
--- patch-invalid-url.yaml --
-spec:
-  url: "postgres://invalid"
 -- config.hcl --
 variable "db_url" {
   type = string
diff --git a/test/e2e/testscript/schema-config-variables.txtar b/test/e2e/testscript/schema-config-variables.txtar
index e1a55bd..adfbde0 100644
--- a/test/e2e/testscript/schema-config-variables.txtar
+++ b/test/e2e/testscript/schema-config-variables.txtar
@@ -20,10 +20,6 @@ kubectl create secret generic schema-config --from-file=config.hcl
 kubectl patch -f schema.yaml --type merge --patch-file patch-schema-config-from-configmap.yaml
 kubectl wait --for=jsonpath='{.status.conditions[*].reason}'=Applied --timeout=500s AtlasSchemas/sample
 
-# Ensure the operator priority the spec url over the config
-kubectl patch -f schema.yaml --type merge --patch-file patch-invalid-url.yaml
-kubectl wait --for=jsonpath='{.status.conditions[*].message}'='"Error: postgres: scanning system variables: pq: Could not detect default username. Please provide one explicitly"' --timeout=500s AtlasSchemas/sample
-
 -- schema.yaml --
 apiVersion: db.atlasgo.io/v1alpha1
 kind: AtlasSchema
@@ -75,9 +71,6 @@ spec:
     secretKeyRef:
       name: schema-config
       key: config.hcl
--- patch-invalid-url.yaml --
-spec:
-  url: "postgres://invalid"
 -- config.hcl --
 variable "db_url" {
   type = string