diff --git a/src/lib/libcore.js b/src/lib/libcore.js
index 46fffb1192829..9143ee827a883 100644
--- a/src/lib/libcore.js
+++ b/src/lib/libcore.js
@@ -2094,8 +2094,13 @@ addToLibrary({
 #endif
       try {
 #if PTHREADS
-        if (ENVIRONMENT_IS_PTHREAD) __emscripten_thread_exit(EXITSTATUS);
-        else
+        if (ENVIRONMENT_IS_PTHREAD) {
+          // exit the current thread, but only if there is one active.
+          // TODO(https://github.com/emscripten-core/emscripten/issues/25076):
+          // Unify this check with the runtimeExited check above
+          if (_pthread_self()) __emscripten_thread_exit(EXITSTATUS);
+          return;
+        }
 #endif
         _exit(EXITSTATUS);
       } catch (e) {
@@ -2113,8 +2118,19 @@ addToLibrary({
   },
 
 #else // MINIMAL_RUNTIME
-  // MINIMAL_RUNTIME doesn't support the runtimeKeepalive stuff
-  $callUserCallback: (func) => func(),
+  $callUserCallback: (func) => {
+    // MINIMAL_RUNTIME doesn't support the runtimeKeepalive stuff, but under
+    // some circumstances it supportes `runtimeExited`
+#if EXIT_RUNTIME
+    if (runtimeExited) {
+#if ASSERTIONS
+      err('user callback triggered after runtime exited or application aborted.  Ignoring.');
+#endif
+      return;
+    }
+#endif
+    func();
+  },
 #endif // MINIMAL_RUNTIME
 
   $asmjsMangle: (x) => {
diff --git a/src/lib/libpthread.js b/src/lib/libpthread.js
index e251f4508ba23..9072ca392ff06 100644
--- a/src/lib/libpthread.js
+++ b/src/lib/libpthread.js
@@ -1094,18 +1094,16 @@ var LibraryPThread = {
     checkStackCookie();
 #endif
     function finish(result) {
-#if MINIMAL_RUNTIME
+#if !MINIMAL_RUNTIME
       // In MINIMAL_RUNTIME the noExitRuntime concept does not apply to
       // pthreads. To exit a pthread with live runtime, use the function
       // emscripten_unwind_to_js_event_loop() in the pthread body.
-      __emscripten_thread_exit(result);
-#else
       if (keepRuntimeAlive()) {
         EXITSTATUS = result;
-      } else {
-        __emscripten_thread_exit(result);
+        return;
       }
 #endif
+      __emscripten_thread_exit(result);
     }
 #if ASYNCIFY == 2
     result = await result;
@@ -1215,9 +1213,14 @@ var LibraryPThread = {
                         'pthread_self',
                         '_emscripten_check_mailbox',
                         '_emscripten_thread_mailbox_await'],
-  $checkMailbox: () => {
+  $checkMailbox: () => callUserCallback(() => {
     // Only check the mailbox if we have a live pthread runtime. We implement
     // pthread_self to return 0 if there is no live runtime.
+    //
+    // TODO(https://github.com/emscripten-core/emscripten/issues/25076):
+    // Is this check still needed?  `callUserCallback` is supposed to
+    // ensure the runtime is alive, and if `_pthread_self` is NULL then the
+    // runtime certainly is *not* alive, so this should be a redundant check.
     var pthread_ptr = _pthread_self();
     if (pthread_ptr) {
       // If we are using Atomics.waitAsync as our notification mechanism, wait
@@ -1225,9 +1228,9 @@ var LibraryPThread = {
       // work that could otherwise arrive after we've finished processing the
       // mailbox and before we're ready for the next notification.
       __emscripten_thread_mailbox_await(pthread_ptr);
-      callUserCallback(__emscripten_check_mailbox);
+      __emscripten_check_mailbox();
     }
-  },
+  }),
 
   _emscripten_thread_mailbox_await__deps: ['$checkMailbox'],
   _emscripten_thread_mailbox_await: (pthread_ptr) => {
diff --git a/test/code_size/test_codesize_minimal_pthreads.json b/test/code_size/test_codesize_minimal_pthreads.json
index d2d287006e49b..65363c9767a11 100644
--- a/test/code_size/test_codesize_minimal_pthreads.json
+++ b/test/code_size/test_codesize_minimal_pthreads.json
@@ -1,10 +1,10 @@
 {
-  "a.out.js": 7649,
-  "a.out.js.gz": 3768,
+  "a.out.js": 7660,
+  "a.out.js.gz": 3776,
   "a.out.nodebug.wasm": 19588,
   "a.out.nodebug.wasm.gz": 9025,
-  "total": 27237,
-  "total_gz": 12793,
+  "total": 27248,
+  "total_gz": 12801,
   "sent": [
     "a (memory)",
     "b (emscripten_get_now)",
diff --git a/test/code_size/test_codesize_minimal_pthreads_memgrowth.json b/test/code_size/test_codesize_minimal_pthreads_memgrowth.json
index 3f98de951b241..cbae98d55659e 100644
--- a/test/code_size/test_codesize_minimal_pthreads_memgrowth.json
+++ b/test/code_size/test_codesize_minimal_pthreads_memgrowth.json
@@ -1,10 +1,10 @@
 {
-  "a.out.js": 8076,
-  "a.out.js.gz": 3974,
+  "a.out.js": 8087,
+  "a.out.js.gz": 3978,
   "a.out.nodebug.wasm": 19589,
   "a.out.nodebug.wasm.gz": 9025,
-  "total": 27665,
-  "total_gz": 12999,
+  "total": 27676,
+  "total_gz": 13003,
   "sent": [
     "a (memory)",
     "b (emscripten_get_now)",
diff --git a/tools/emscripten.py b/tools/emscripten.py
index 112e7eeb77d06..7dd9853f2e041 100644
--- a/tools/emscripten.py
+++ b/tools/emscripten.py
@@ -897,9 +897,7 @@ def install_debug_wrapper(sym):
     return False
   # Likewise `__trap` can occur before the runtime is initialized since it is used in
   # abort.
-  # pthread_self is currently called in some cases after the runtime has exited.
-  # TODO: Look into removing these, and improving our robustness around thread termination.
-  return sym not in {'__trap', 'pthread_self'}
+  return sym != '__trap'
 
 
 def should_export(sym):