diff --git a/app/include/zmk/matrix.h b/app/include/zmk/matrix.h
index e38f5a4967c..436f86f5d18 100644
--- a/app/include/zmk/matrix.h
+++ b/app/include/zmk/matrix.h
@@ -13,10 +13,6 @@
 
 #if DT_HAS_COMPAT_STATUS_OKAY(zmk_physical_layout)
 
-#if ZMK_MATRIX_HAS_TRANSFORM
-#error "To use physical layouts, remove the chosen `zmk,matrix-transform` value."
-#endif
-
 #define ZMK_PHYSICAL_LAYOUT_BYTE_ARRAY(node_id)                                                    \
     uint8_t _CONCAT(prop_, node_id)[DT_PROP_LEN(DT_PHANDLE(node_id, transform), map)];
 
diff --git a/app/src/physical_layouts.c b/app/src/physical_layouts.c
index e77a290ed13..c71b427a4dd 100644
--- a/app/src/physical_layouts.c
+++ b/app/src/physical_layouts.c
@@ -24,7 +24,10 @@ LOG_MODULE_DECLARE(zmk, CONFIG_ZMK_LOG_LEVEL);
 
 #define DT_DRV_COMPAT zmk_physical_layout
 
-#if DT_HAS_COMPAT_STATUS_OKAY(DT_DRV_COMPAT)
+#define USE_PHY_LAYOUTS                                                                            \
+    (DT_HAS_COMPAT_STATUS_OKAY(DT_DRV_COMPAT) && !DT_HAS_CHOSEN(zmk_matrix_transform))
+
+#if USE_PHY_LAYOUTS
 
 #define ZKPA_INIT(i, n)                                                                            \
     (const struct zmk_key_physical_attrs) {                                                        \
@@ -99,6 +102,13 @@ static const struct zmk_physical_layout *const layouts[] = {
 
 #elif DT_HAS_CHOSEN(zmk_matrix_transform)
 
+#if DT_HAS_COMPAT_STATUS_OKAY(DT_DRV_COMPAT)
+
+#warning                                                                                           \
+    "Ignoring the physical layouts and using the chosen matrix transform. Consider setting a chosen physical layout instead."
+
+#endif
+
 ZMK_MATRIX_TRANSFORM_EXTERN(DT_CHOSEN(zmk_matrix_transform));
 
 static const struct zmk_physical_layout _CONCAT(_zmk_physical_layout_, chosen) = {
@@ -111,6 +121,13 @@ static const struct zmk_physical_layout *const layouts[] = {
 
 #elif DT_HAS_CHOSEN(zmk_kscan)
 
+#if DT_HAS_COMPAT_STATUS_OKAY(DT_DRV_COMPAT)
+
+#warning                                                                                           \
+    "Ignoring the physical layouts and using the chosen kscan with a synthetic transform. Consider setting a chosen physical layout instead."
+
+#endif
+
 ZMK_MATRIX_TRANSFORM_DEFAULT_EXTERN();
 static const struct zmk_physical_layout _CONCAT(_zmk_physical_layout_, chosen) = {
     .display_name = "Default",
@@ -252,7 +269,7 @@ static int8_t saved_selected_index = -1;
 int zmk_physical_layouts_select_initial(void) {
     const struct zmk_physical_layout *initial;
 
-#if DT_HAS_CHOSEN(zmk_physical_layout)
+#if USE_PHY_LAYOUTS && DT_HAS_CHOSEN(zmk_physical_layout)
     initial = &_CONCAT(_zmk_physical_layout_, DT_CHOSEN(zmk_physical_layout));
 #else
     initial = layouts[0];