diff --git a/ports/esp32/main.c b/ports/esp32/main.c
index 03dc0807a025c..f360a044f2599 100644
--- a/ports/esp32/main.c
+++ b/ports/esp32/main.c
@@ -49,6 +49,7 @@
 #include "py/repl.h"
 #include "py/gc.h"
 #include "py/mphal.h"
+#include "py/objmodule.h"
 #include "shared/readline/readline.h"
 #include "shared/runtime/pyexec.h"
 #include "shared/timeutils/timeutils.h"
@@ -182,6 +183,10 @@ void mp_task(void *pvParameter) {
     mp_thread_deinit();
     #endif
 
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
+
     gc_sweep_all();
 
     // Free any native code pointers that point to iRAM.
diff --git a/ports/esp8266/main.c b/ports/esp8266/main.c
index 2dd7c1dece3a4..cd6540a7a925d 100644
--- a/ports/esp8266/main.c
+++ b/ports/esp8266/main.c
@@ -35,6 +35,7 @@
 #include "py/mperrno.h"
 #include "py/mphal.h"
 #include "py/gc.h"
+#include "py/objmodule.h"
 
 #include "extmod/misc.h"
 #include "extmod/modmachine.h"
@@ -88,6 +89,9 @@ static void mp_reset(void) {
 }
 
 void soft_reset(void) {
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
     gc_sweep_all();
     mp_hal_stdout_tx_str("MPY: soft reboot\r\n");
     mp_hal_delay_us(10000); // allow UART to flush output
diff --git a/ports/mimxrt/main.c b/ports/mimxrt/main.c
index adb071a7fee8f..282789875ca23 100644
--- a/ports/mimxrt/main.c
+++ b/ports/mimxrt/main.c
@@ -30,6 +30,7 @@
 #include "py/gc.h"
 #include "py/mperrno.h"
 #include "py/stackctrl.h"
+#include "py/objmodule.h"
 #include "shared/readline/readline.h"
 #include "shared/runtime/gchelper.h"
 #include "shared/runtime/pyexec.h"
@@ -159,6 +160,9 @@ int main(void) {
         machine_uart_deinit_all();
         machine_pwm_deinit_all();
         soft_timer_deinit();
+        #if MICROPY_PY_SYS_ATEXIT
+        mp_sys_atexit_execute();
+        #endif
         gc_sweep_all();
         mp_deinit();
     }
diff --git a/ports/nrf/main.c b/ports/nrf/main.c
index 29550bd77a748..1ca023c3fa934 100644
--- a/ports/nrf/main.c
+++ b/ports/nrf/main.c
@@ -35,6 +35,7 @@
 #include "py/lexer.h"
 #include "py/parse.h"
 #include "py/obj.h"
+#include "py/objmodule.h"
 #include "py/runtime.h"
 #include "py/stackctrl.h"
 #include "py/gc.h"
@@ -292,6 +293,11 @@ void NORETURN _start(void) {
     pwm_deinit_all();
     #endif
 
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
+
+    gc_sweep_all();
     mp_deinit();
 
     printf("MPY: soft reboot\n");
diff --git a/ports/qemu/main.c b/ports/qemu/main.c
index 042106580407d..6b9a8c919ae60 100644
--- a/ports/qemu/main.c
+++ b/ports/qemu/main.c
@@ -31,6 +31,7 @@
 #include "py/stackctrl.h"
 #include "py/gc.h"
 #include "py/mperrno.h"
+#include "py/objmodule.h"
 #include "shared/runtime/gchelper.h"
 #include "shared/runtime/pyexec.h"
 
@@ -60,6 +61,9 @@ int main(int argc, char **argv) {
 
         mp_printf(&mp_plat_print, "MPY: soft reboot\n");
 
+        #if MICROPY_PY_SYS_ATEXIT
+        mp_sys_atexit_execute();
+        #endif
         gc_sweep_all();
         mp_deinit();
     }
diff --git a/ports/renesas-ra/main.c b/ports/renesas-ra/main.c
index febb7b6d7aaa3..bba7254826bf4 100644
--- a/ports/renesas-ra/main.c
+++ b/ports/renesas-ra/main.c
@@ -33,6 +33,7 @@
 #include "py/gc.h"
 #include "py/mperrno.h"
 #include "py/mphal.h"
+#include "py/objmodule.h"
 #include "shared/readline/readline.h"
 #include "shared/runtime/pyexec.h"
 #include "shared/runtime/softtimer.h"
@@ -435,6 +436,10 @@ int main(void) {
     pyb_thread_deinit();
     #endif
 
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
+
     MICROPY_BOARD_END_SOFT_RESET(&state);
 
     gc_sweep_all();
diff --git a/ports/rp2/main.c b/ports/rp2/main.c
index d6bf448267152..676907988fb47 100644
--- a/ports/rp2/main.c
+++ b/ports/rp2/main.c
@@ -32,6 +32,7 @@
 #include "py/gc.h"
 #include "py/mperrno.h"
 #include "py/mphal.h"
+#include "py/objmodule.h"
 #include "extmod/modbluetooth.h"
 #include "extmod/modnetwork.h"
 #include "shared/readline/readline.h"
@@ -241,6 +242,9 @@ int main(int argc, char **argv) {
         #if MICROPY_HW_ENABLE_USB_RUNTIME_DEVICE
         mp_usbd_deinit();
         #endif
+        #if MICROPY_PY_SYS_ATEXIT
+        mp_sys_atexit_execute();
+        #endif
 
         // Hook for resetting anything right at the end of a soft reset command.
         MICROPY_BOARD_END_SOFT_RESET();
diff --git a/ports/samd/main.c b/ports/samd/main.c
index 2bbaf63e6e4c5..c5ab8e7ca2dfe 100644
--- a/ports/samd/main.c
+++ b/ports/samd/main.c
@@ -29,6 +29,7 @@
 #include "py/gc.h"
 #include "py/mperrno.h"
 #include "py/stackctrl.h"
+#include "py/objmodule.h"
 #include "shared/readline/readline.h"
 #include "shared/runtime/gchelper.h"
 #include "shared/runtime/pyexec.h"
@@ -98,6 +99,9 @@ void samd_main(void) {
         #if MICROPY_HW_ENABLE_USB_RUNTIME_DEVICE
         mp_usbd_deinit();
         #endif
+        #if MICROPY_PY_SYS_ATEXIT
+        mp_sys_atexit_execute();
+        #endif
         gc_sweep_all();
         #if MICROPY_PY_MACHINE_I2C || MICROPY_PY_MACHINE_SPI || MICROPY_PY_MACHINE_UART
         sercom_deinit_all();
diff --git a/ports/stm32/main.c b/ports/stm32/main.c
index df483602dc901..529cd9e51e3ba 100644
--- a/ports/stm32/main.c
+++ b/ports/stm32/main.c
@@ -32,6 +32,7 @@
 #include "py/gc.h"
 #include "py/mperrno.h"
 #include "py/mphal.h"
+#include "py/objmodule.h"
 #include "shared/readline/readline.h"
 #include "shared/runtime/pyexec.h"
 #include "shared/runtime/softtimer.h"
@@ -698,6 +699,10 @@ void stm32_main(uint32_t reset_mode) {
     MP_STATE_PORT(pyb_stdio_uart) = NULL;
     #endif
 
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
+
     MICROPY_BOARD_END_SOFT_RESET(&state);
 
     gc_sweep_all();
diff --git a/ports/unix/main.c b/ports/unix/main.c
index 58fa3ff589a55..e8f8960a0525a 100644
--- a/ports/unix/main.c
+++ b/ports/unix/main.c
@@ -43,6 +43,7 @@
 #include "py/builtin.h"
 #include "py/repl.h"
 #include "py/gc.h"
+#include "py/objmodule.h"
 #include "py/objstr.h"
 #include "py/cstack.h"
 #include "py/mphal.h"
@@ -753,10 +754,7 @@ MP_NOINLINE int main_(int argc, char **argv) {
     #endif
 
     #if MICROPY_PY_SYS_ATEXIT
-    // Beware, the sys.settrace callback should be disabled before running sys.atexit.
-    if (mp_obj_is_callable(MP_STATE_VM(sys_exitfunc))) {
-        mp_call_function_0(MP_STATE_VM(sys_exitfunc));
-    }
+    mp_sys_atexit_execute();
     #endif
 
     #if MICROPY_PY_MICROPYTHON_MEM_INFO
diff --git a/ports/zephyr/main.c b/ports/zephyr/main.c
index 9fae2b3a873e5..4f482a1319cc1 100644
--- a/ports/zephyr/main.c
+++ b/ports/zephyr/main.c
@@ -48,6 +48,7 @@
 #include "py/gc.h"
 #include "py/mphal.h"
 #include "py/stackctrl.h"
+#include "py/objmodule.h"
 #include "shared/runtime/gchelper.h"
 #include "shared/runtime/pyexec.h"
 #include "shared/readline/readline.h"
@@ -172,6 +173,10 @@ int real_main(void) {
     gc_collect();
     #endif
 
+    #if MICROPY_PY_SYS_ATEXIT
+    mp_sys_atexit_execute();
+    #endif
+
     gc_sweep_all();
     mp_deinit();