diff --git a/common/bootmagic.c b/common/bootmagic.c
index 311a02f2..0baff830 100644
--- a/common/bootmagic.c
+++ b/common/bootmagic.c
@@ -7,6 +7,7 @@
 #include "keymap.h"
 #include "action_layer.h"
 #include "eeconfig.h"
+#include "keymap_in_eeprom.h"
 #include "bootmagic.h"
 
 
@@ -30,8 +31,10 @@ void bootmagic(void)
 
     /* eeconfig clear */
     if (bootmagic_scan_keycode(BOOTMAGIC_KEY_EEPROM_CLEAR)) {
-        eeconfig_disable();
         eeconfig_init();
+#ifdef KEYMAP_IN_EEPROM_ENABLE
+        write_keymap_to_eeprom();
+#endif
     }
 
     /* bootloader */
diff --git a/common/eeconfig.c b/common/eeconfig.c
index d98cd61a..5bd47dc6 100644
--- a/common/eeconfig.c
+++ b/common/eeconfig.c
@@ -2,7 +2,6 @@
 #include <stdbool.h>
 #include <avr/eeprom.h>
 #include "eeconfig.h"
-#include "keymap_in_eeprom.h"
 
 void eeconfig_init(void)
 {
@@ -14,9 +13,6 @@ void eeconfig_init(void)
 #ifdef BACKLIGHT_ENABLE
     eeprom_write_byte(EECONFIG_BACKLIGHT,      0);
 #endif
-#ifdef KEYMAP_IN_EEPROM_ENABLE
-    keymap_in_eeprom_init();
-#endif
 }
 
 void eeconfig_enable(void)
@@ -27,9 +23,6 @@ void eeconfig_enable(void)
 void eeconfig_disable(void)
 {
     eeprom_write_word(EECONFIG_MAGIC, 0xFFFF);
-#ifdef KEYMAP_IN_EEPROM_ENABLE
-    keymap_in_eeprom_disable();
-#endif
 }
 
 bool eeconfig_is_enabled(void)