diff --git a/common/bootmagic.c b/common/bootmagic.c
index 036d4904..311a02f2 100644
--- a/common/bootmagic.c
+++ b/common/bootmagic.c
@@ -30,6 +30,7 @@ void bootmagic(void)
 
     /* eeconfig clear */
     if (bootmagic_scan_keycode(BOOTMAGIC_KEY_EEPROM_CLEAR)) {
+        eeconfig_disable();
         eeconfig_init();
     }
 
diff --git a/common/eeconfig.c b/common/eeconfig.c
index 5bd47dc6..5aadf1c5 100644
--- a/common/eeconfig.c
+++ b/common/eeconfig.c
@@ -2,6 +2,7 @@
 #include <stdbool.h>
 #include <avr/eeprom.h>
 #include "eeconfig.h"
+#include "keymap_ex.h"
 
 void eeconfig_init(void)
 {
@@ -13,6 +14,9 @@ void eeconfig_init(void)
 #ifdef BACKLIGHT_ENABLE
     eeprom_write_byte(EECONFIG_BACKLIGHT,      0);
 #endif
+#ifdef KEYMAP_EX_ENABLE
+    keymap_ex_init();
+#endif
 }
 
 void eeconfig_enable(void)
@@ -22,6 +26,9 @@ void eeconfig_enable(void)
 
 void eeconfig_disable(void)
 {
+#ifdef KEYMAP_EX_ENABLE
+    keymap_ex_disable();
+#endif
     eeprom_write_word(EECONFIG_MAGIC, 0xFFFF);
 }
 
diff --git a/common/keymap_ex.c b/common/keymap_ex.c
index 0c01f707..99859c06 100644
--- a/common/keymap_ex.c
+++ b/common/keymap_ex.c
@@ -23,12 +23,16 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #ifdef KEYMAP_EX_ENABLE
 
-void keymap_init(void) {
+void keymap_ex_init(void) {
     if (!check_keymap_in_eeprom()) {
         write_keymap_to_eeprom();
     }
 }
 
+void keymap_ex_disable(void) {
+    eeprom_write_word((void*)EECONFIG_KEYMAP_CHECKSUM, eeprom_read_word((void*)EECONFIG_KEYMAP_CHECKSUM) + 1);
+}
+
 bool check_keymap_in_eeprom(void) {
     uint16_t checksum_in_eeprom = eeprom_read_word(&((keymap_ex_t*)EECONFIG_KEYMAP_EX)->checksum);
     uint16_t checksum = EECONFIG_MAGIC_NUMBER;
diff --git a/common/keymap_ex.h b/common/keymap_ex.h
index e64bace6..ee6ff8c6 100644
--- a/common/keymap_ex.h
+++ b/common/keymap_ex.h
@@ -47,7 +47,8 @@ typedef struct {
 #define FN_ACTION_OFFSET(index) (sizeof(uint16_t) * index)
 #define KEY_OFFSET(layer, row, col) (sizeof(uint8_t) * (layer * MATRIX_ROWS * MATRIX_COLS + row * MATRIX_COLS + col))
 
-void keymap_init(void);
+void keymap_ex_init(void);
+void keymap_ex_disable(void);
 bool check_keymap_in_eeprom(void);
 void write_keymap_to_eeprom(void);
 uint8_t eeconfig_read_keymap_key(uint8_t layer, uint8_t row, uint8_t col);