diff --git a/ports/unix/btstack_usb.c b/ports/unix/btstack_usb.c
index 76f32d6d27..ab6a49f39a 100644
--- a/ports/unix/btstack_usb.c
+++ b/ports/unix/btstack_usb.c
@@ -156,7 +156,10 @@ STATIC void *btstack_thread(void *arg) {
     // Or, if a timeout results in it being set to TIMEOUT.
 
     while (mp_bluetooth_btstack_state == MP_BLUETOOTH_BTSTACK_STATE_STARTING || mp_bluetooth_btstack_state == MP_BLUETOOTH_BTSTACK_STATE_ACTIVE) {
+        // Pretend like we're running in IRQ context (i.e. other things can't be running at the same time).
+        mp_uint_t atomic_state = MICROPY_BEGIN_ATOMIC_SECTION();
         btstack_run_loop_embedded_execute_once();
+        MICROPY_END_ATOMIC_SECTION(atomic_state);
 
         // The USB transport schedules events to the run loop at 1ms intervals,
         // and the implementation currently polls rather than selects.
diff --git a/ports/unix/mpthreadport.c b/ports/unix/mpthreadport.c
index 711cf2a6bb..de0f5923ba 100644
--- a/ports/unix/mpthreadport.c
+++ b/ports/unix/mpthreadport.c
@@ -65,7 +65,7 @@ STATIC pthread_key_t tls_key;
 // The mutex is used for any code in this port that needs to be thread safe.
 // Specifically for thread management, access to the linked list is one example.
 // But also, e.g. scheduler state.
-STATIC pthread_mutex_t thread_mutex = PTHREAD_MUTEX_INITIALIZER;
+STATIC pthread_mutex_t thread_mutex;
 STATIC thread_t *thread;
 
 // this is used to synchronise the signal handler of the thread
@@ -111,6 +111,13 @@ void mp_thread_init(void) {
     pthread_key_create(&tls_key, NULL);
     pthread_setspecific(tls_key, &mp_state_ctx.thread);
 
+    // Needs to be a recursive mutex to emulate the behavior of
+    // BEGIN_ATOMIC_SECTION on bare metal.
+    pthread_mutexattr_t thread_mutex_attr;
+    pthread_mutexattr_init(&thread_mutex_attr);
+    pthread_mutexattr_settype(&thread_mutex_attr, PTHREAD_MUTEX_RECURSIVE);
+    pthread_mutex_init(&thread_mutex, &thread_mutex_attr);
+
     // create first entry in linked list of all threads
     thread = malloc(sizeof(thread_t));
     thread->id = pthread_self();