diff --git a/libraries/AP_HAL_ChibiOS/HAL_ChibiOS_Class.cpp b/libraries/AP_HAL_ChibiOS/HAL_ChibiOS_Class.cpp
index 31eb71ead9..1eb3c0c647 100644
--- a/libraries/AP_HAL_ChibiOS/HAL_ChibiOS_Class.cpp
+++ b/libraries/AP_HAL_ChibiOS/HAL_ChibiOS_Class.cpp
@@ -261,7 +261,7 @@ static void main_loop()
 #if !defined(DISABLE_WATCHDOG)
 #ifdef IOMCU_FW
     stm32_watchdog_init();
-#elif !defined(HAL_BOOTLOADER_BUILD)
+#else
     // setup watchdog to reset if main loop stops
     if (AP_BoardConfig::watchdog_enabled()) {
         stm32_watchdog_init();
diff --git a/libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py b/libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py
index 60b2024f83..ffc116d669 100644
--- a/libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py
+++ b/libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py
@@ -1113,6 +1113,7 @@ def write_mcu_config(f):
 #define HAL_USE_EMPTY_STORAGE 1
 #ifndef HAL_STORAGE_SIZE
 #define HAL_STORAGE_SIZE 16384
+#define DISABLE_WATCHDOG 1
 #endif
 ''')
         else:
@@ -1149,6 +1150,7 @@ def write_mcu_config(f):
 #define HAL_USE_RTC FALSE
 #define DISABLE_SERIAL_ESC_COMM TRUE
 #define CH_CFG_USE_DYNAMIC FALSE
+#define DISABLE_WATCHDOG 1
 ''')
         if not env_vars['EXT_FLASH_SIZE_MB'] and not args.signed_fw:
             f.write('''