diff --git a/lib/utils/pyexec.c b/lib/utils/pyexec.c
index 747097f157..0c9e9791c1 100644
--- a/lib/utils/pyexec.c
+++ b/lib/utils/pyexec.c
@@ -107,6 +107,7 @@ STATIC int parse_compile_execute(const void *source, mp_parse_input_kind_t input
         #endif
         mp_call_function_0(module_fun);
         mp_hal_set_interrupt_char(-1); // disable interrupt
+        mp_handle_pending(true); // handle any pending exceptions (and any callbacks)
         nlr_pop();
         ret = 1;
         if (exec_flags & EXEC_FLAG_PRINT_EOF) {
@@ -114,8 +115,8 @@ STATIC int parse_compile_execute(const void *source, mp_parse_input_kind_t input
         }
     } else {
         // uncaught exception
-        // FIXME it could be that an interrupt happens just before we disable it here
         mp_hal_set_interrupt_char(-1); // disable interrupt
+        mp_handle_pending(false); // clear any pending exceptions (and run any callbacks)
         // print EOF after normal output
         if (exec_flags & EXEC_FLAG_PRINT_EOF) {
             mp_hal_stdout_tx_strn("\x04", 1);
diff --git a/ports/unix/main.c b/ports/unix/main.c
index 3f415285cb..7a3305a5dc 100644
--- a/ports/unix/main.c
+++ b/ports/unix/main.c
@@ -145,21 +145,17 @@ STATIC int execute_from_lexer(int source_kind, const void *source, mp_parse_inpu
         if (!compile_only) {
             // execute it
             mp_call_function_0(module_fun);
-            // check for pending exception
-            if (MP_STATE_VM(mp_pending_exception) != MP_OBJ_NULL) {
-                mp_obj_t obj = MP_STATE_VM(mp_pending_exception);
-                MP_STATE_VM(mp_pending_exception) = MP_OBJ_NULL;
-                nlr_raise(obj);
-            }
         }
 
         mp_hal_set_interrupt_char(-1);
+        mp_handle_pending(true);
         nlr_pop();
         return 0;
 
     } else {
         // uncaught exception
         mp_hal_set_interrupt_char(-1);
+        mp_handle_pending(false);
         return handle_uncaught_exception(nlr.ret_val);
     }
 }