diff --git a/core/core-configuration-layer.el b/core/core-configuration-layer.el
index 2524f6e7b..55e893eee 100644
--- a/core/core-configuration-layer.el
+++ b/core/core-configuration-layer.el
@@ -662,6 +662,9 @@ To prevent package from being installed or uninstalled set the variable
         (configuration-layer/delete-orphan-packages packages))))
   ;; configure used packages
   (configuration-layer//configure-packages configuration-layer--used-packages)
+  ;; evaluate layer variables a second time to override default values set in
+  ;; packages configuration above
+  (configuration-layer//set-layers-variables configuration-layer--used-layers)
   (configuration-layer//load-layers-files configuration-layer--used-layers
                         '("keybindings.el"))
   (dotspacemacs|call-func dotspacemacs/user-load
@@ -1558,9 +1561,10 @@ RNAME is the name symbol of another existing layer."
          "Unknown layer %s to declare lshadow relationship."
          rname)))))
 
-(defun configuration-layer//set-layers-variables (layers)
-  "Set the configuration variables for the passed LAYERS."
-  (mapc 'configuration-layer//set-layer-variables layers))
+(defun configuration-layer//set-layers-variables (layer-names)
+  "Set the configuration variables for the passed LAYER-NAMES."
+  (mapc 'configuration-layer//set-layer-variables (mapcar '(lambda (lname) (configuration-layer/get-layer lname))
+                                        layer-names)))
 
 (defun configuration-layer//set-layer-variables (layer)
   "Set the configuration variables for the passed LAYER."
diff --git a/tests/core/core-configuration-layer-utest.el b/tests/core/core-configuration-layer-utest.el
index d94fcccfd..6eeaa3c7a 100644
--- a/tests/core/core-configuration-layer-utest.el
+++ b/tests/core/core-configuration-layer-utest.el
@@ -1151,47 +1151,55 @@
 ;; ---------------------------------------------------------------------------
 
 (ert-deftest test-set-layers-variables--none ()
-  (let ((input `(,(cfgl-layer "layer"
-                              :name 'layer
-                              :dir "/a/path/")))
+  (let ((configuration-layer--indexed-layers (make-hash-table :size 1024))
         (var 'foo))
-    (configuration-layer//set-layers-variables input)
+    (helper--add-layers
+     `(,(cfgl-layer "layer"
+                    :name 'layer
+                    :dir "/a/path/")))
+    (configuration-layer//set-layers-variables '(layer))
     (should (eq var 'foo))))
 
 (ert-deftest test-set-layers-variables--one-value ()
-  (let ((input `(,(cfgl-layer "layer"
-                              :name 'layer
-                              :dir "/a/path/"
-                              :variables '(var1 'bar)))))
+  (let ((configuration-layer--indexed-layers (make-hash-table :size 1024)))
+    (helper--add-layers
+     `(,(cfgl-layer "layer"
+                    :name 'layer
+                    :dir "/a/path/"
+                    :variables '(var1 'bar))))
     (setq var1 'foo)
-    (configuration-layer//set-layers-variables input)
+    (configuration-layer//set-layers-variables '(layer))
     (should (eq var1 'bar))))
 
 (ert-deftest test-set-layers-variables--multiple-values ()
-  (let ((input `(,(cfgl-layer "layer"
-                              :name 'layer
-                              :dir "/a/path/"
-                              :variables '(var1 'bar1 var2 'bar2 var3 'bar3)))))
+  (let ((configuration-layer--indexed-layers (make-hash-table :size 1024)))
+    (helper--add-layers
+     `(,(cfgl-layer "layer"
+                    :name 'layer
+                    :dir "/a/path/"
+                    :variables '(var1 'bar1 var2 'bar2 var3 'bar3))))
     (setq var1 'foo)
     (setq var2 'foo)
     (setq var3 'foo)
-    (configuration-layer//set-layers-variables input)
+    (configuration-layer//set-layers-variables '(layer))
     (should (eq var1 'bar1))
     (should (eq var2 'bar2))
     (should (eq var3 'bar3))))
 
 (ert-deftest test-set-layers-variables--odd-number-of-values ()
-  (let ((input `(,(cfgl-layer "layer"
-                              :name 'layer
-                              :dir "/a/path/"
-                              :variables '(var1 'bar var2)))))
+  (let ((configuration-layer--indexed-layers (make-hash-table :size 1024)))
+    (helper--add-layers
+     `(,(cfgl-layer "layer"
+                    :name 'layer
+                    :dir "/a/path/"
+                    :variables '(var1 'bar var2))))
     (mocker-let
      ((configuration-layer//warning
        (msg &rest args)
        ((:record-cls 'mocker-stub-record :output nil :occur 1))))
      (setq var1 'foo)
      (setq var2 'foo)
-     (configuration-layer//set-layers-variables input)
+     (configuration-layer//set-layers-variables '(layer))
      (should (eq var1 'bar))
      (should (eq var2 'foo)))))