diff --git a/emcc.py b/emcc.py
index 9fbc00070dc63..d7e8606e0bbdd 100755
--- a/emcc.py
+++ b/emcc.py
@@ -2336,6 +2336,9 @@ def check_memory_setting(setting):
     # always does.
     settings.DEFAULT_LIBRARY_FUNCS_TO_INCLUDE += ['$callRuntimeCallbacks']
 
+  if settings.EXIT_RUNTIME and not settings.STANDALONE_WASM:
+    settings.REQUIRED_EXPORTS += ['__funcs_on_exit']
+
   # various settings require malloc/free support from JS
   if settings.RELOCATABLE or \
      settings.BUILD_AS_WORKER or \
diff --git a/src/library.js b/src/library.js
index 48db674a48762..3f773fcababfc 100644
--- a/src/library.js
+++ b/src/library.js
@@ -361,21 +361,6 @@ LibraryManager.library = {
   // stdlib.h
   // ==========================================================================
 
-#if MINIMAL_RUNTIME && !EXIT_RUNTIME
-  atexit__sig: 'v', // atexit unsupported in MINIMAL_RUNTIME
-  atexit: function(){},
-  __cxa_atexit: function(){},
-#else
-  atexit__proxy: 'sync',
-  atexit__sig: 'iii',
-  atexit: function(func, arg) {
-#if EXIT_RUNTIME
-    __ATEXIT__.unshift({ func: func, arg: arg });
-#endif
-  },
-  __cxa_atexit: 'atexit',
-#endif
-
   // TODO: There are currently two abort() functions that get imported to asm
   // module scope: the built-in runtime function abort(), and this library
   // function _abort(). Remove one of these, importing two functions for the
diff --git a/src/preamble.js b/src/preamble.js
index 5ba9b3967c38f..dcdcc5335cce3 100644
--- a/src/preamble.js
+++ b/src/preamble.js
@@ -430,6 +430,9 @@ function exitRuntime() {
   if (ENVIRONMENT_IS_PTHREAD) return; // PThreads reuse the runtime from the main thread.
 #endif
 #if EXIT_RUNTIME
+#if !STANDALONE_WASM
+  ___funcs_on_exit(); // Native atexit() functions
+#endif
   callRuntimeCallbacks(__ATEXIT__);
   <<< ATEXITS >>>
 #endif
diff --git a/system/lib/libc/atexit_dummy.c b/system/lib/libc/atexit_dummy.c
new file mode 100644
index 0000000000000..f7969fe72bb6d
--- /dev/null
+++ b/system/lib/libc/atexit_dummy.c
@@ -0,0 +1,18 @@
+/*
+ * Copyright 2022 The Emscripten Authors.  All rights reserved.
+ * Emscripten is available under two separate licenses, the MIT license and the
+ * University of Illinois/NCSA Open Source License.  Both these licenses can be
+ * found in the LICENSE file.
+ */
+
+// Stub implementations of atexit function.  These will be included
+// in favor of the regular ones in system/lib/libc/musl/src/exit/atexit.c
+// when EXIT_RUNTIME == 0.
+
+#include <stdlib.h>
+
+int atexit(void (*function)(void)) { return 0; }
+
+int __cxa_atexit(void (*func)(void *), void *arg, void *dso) { return 0; }
+
+void __cxa_finalize(void *dso) { }
diff --git a/tests/other/metadce/hello_libcxx_O2.jssize b/tests/other/metadce/hello_libcxx_O2.jssize
index a71fabff39235..a1de4ec547adf 100644
--- a/tests/other/metadce/hello_libcxx_O2.jssize
+++ b/tests/other/metadce/hello_libcxx_O2.jssize
@@ -1 +1 @@
-98361
+98236
diff --git a/tests/other/metadce/hello_libcxx_O2.sent b/tests/other/metadce/hello_libcxx_O2.sent
index 943c0ca713dc4..25e3f929f2fb9 100644
--- a/tests/other/metadce/hello_libcxx_O2.sent
+++ b/tests/other/metadce/hello_libcxx_O2.sent
@@ -1,4 +1,3 @@
-__cxa_atexit
 abort
 emscripten_memcpy_big
 emscripten_resize_heap
diff --git a/tests/other/metadce/hello_libcxx_O2_fexceptions.jssize b/tests/other/metadce/hello_libcxx_O2_fexceptions.jssize
index 6d7849572b30b..f02cad118882c 100644
--- a/tests/other/metadce/hello_libcxx_O2_fexceptions.jssize
+++ b/tests/other/metadce/hello_libcxx_O2_fexceptions.jssize
@@ -1 +1 @@
-111833
+111708
diff --git a/tests/other/metadce/hello_libcxx_O2_fexceptions.sent b/tests/other/metadce/hello_libcxx_O2_fexceptions.sent
index 21c54d195a506..354d1ea99aa90 100644
--- a/tests/other/metadce/hello_libcxx_O2_fexceptions.sent
+++ b/tests/other/metadce/hello_libcxx_O2_fexceptions.sent
@@ -1,5 +1,4 @@
 __cxa_allocate_exception
-__cxa_atexit
 __cxa_begin_catch
 __cxa_end_catch
 __cxa_find_matching_catch_2
diff --git a/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.jssize b/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.jssize
index 6ae4b778e8663..83b6b5bb3fa12 100644
--- a/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.jssize
+++ b/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.jssize
@@ -1 +1 @@
-112820
+112695
diff --git a/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.sent b/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.sent
index 21c54d195a506..354d1ea99aa90 100644
--- a/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.sent
+++ b/tests/other/metadce/hello_libcxx_O2_fexceptions_DEMANGLE_SUPPORT.sent
@@ -1,5 +1,4 @@
 __cxa_allocate_exception
-__cxa_atexit
 __cxa_begin_catch
 __cxa_end_catch
 __cxa_find_matching_catch_2
diff --git a/tests/pthread/test_pthread_busy_wait_atexit.cpp b/tests/pthread/test_pthread_busy_wait_atexit.cpp
new file mode 100644
index 0000000000000..64d0c0769ee2b
--- /dev/null
+++ b/tests/pthread/test_pthread_busy_wait_atexit.cpp
@@ -0,0 +1,37 @@
+#include <stdatomic.h>
+#include <stdbool.h>
+#include <pthread.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <emscripten/console.h>
+
+_Atomic bool done = false;
+
+void exit_handler() {
+  printf("exit_handler\n");
+}
+
+void* thread_main(void*) {
+  // Avoid using printf here since stdio is proxies back to the
+  // main thread which is busy looping
+  _emscripten_out("in thread");
+  atexit(exit_handler);
+  done = true;
+  return NULL;
+}
+
+// Similar to test_pthread_busy_wait.cpp but with lower level pthreads
+// API and explcit use of atexit before setting done to true.
+// We also don't make any calls during the busy loop which means that
+// proxied calls are *not* processed.
+int main() {
+  printf("in main\n");
+  pthread_t t;
+  pthread_create(&t, NULL, thread_main, NULL);
+
+  while (!done) { }
+
+  pthread_join(t, NULL);
+  printf("done main\n");
+  return 0;
+}
diff --git a/tests/pthread/test_pthread_busy_wait_atexit.out b/tests/pthread/test_pthread_busy_wait_atexit.out
new file mode 100644
index 0000000000000..0186ee703018f
--- /dev/null
+++ b/tests/pthread/test_pthread_busy_wait_atexit.out
@@ -0,0 +1,4 @@
+in main
+in thread
+done main
+exit_handler
diff --git a/tests/test_core.py b/tests/test_core.py
index 62ef59f700a81..d30d43a47d7e1 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -8488,6 +8488,12 @@ def test_pthread_busy_wait(self):
     self.set_setting('EXIT_RUNTIME')
     self.do_run_in_out_file_test('pthread/test_pthread_busy_wait.cpp')
 
+  @node_pthreads
+  def test_pthread_busy_wait_atexit(self):
+    self.set_setting('PTHREAD_POOL_SIZE', 1)
+    self.set_setting('EXIT_RUNTIME')
+    self.do_run_in_out_file_test('pthread/test_pthread_busy_wait_atexit.cpp')
+
   @node_pthreads
   def test_pthread_create_pool(self):
     # with a pool, we can synchronously depend on workers being available
diff --git a/tools/system_libs.py b/tools/system_libs.py
index 9cd48739a2220..47cad9824b7a4 100644
--- a/tools/system_libs.py
+++ b/tools/system_libs.py
@@ -760,6 +760,12 @@ class libcompiler_rt(MTLibrary, SjLjLibrary):
       ])
 
 
+class libnoexit(Library):
+  name = 'libnoexit'
+  src_dir = 'system/lib/libc'
+  src_files = ['atexit_dummy.c']
+
+
 class libc(DebugLibrary, AsanInstrumentedLibrary, MuslInternalLibrary, MTLibrary):
   name = 'libc'
 
@@ -918,7 +924,7 @@ def get_files(self):
 
     libc_files += files_in_path(
         path='system/lib/libc/musl/src/exit',
-        filenames=['_Exit.c'])
+        filenames=['_Exit.c', 'atexit.c'])
 
     libc_files += files_in_path(
         path='system/lib/libc/musl/src/ldso',
@@ -1562,7 +1568,7 @@ def get_files(self):
     # including fprintf etc.
     files += files_in_path(
         path='system/lib/libc/musl/src/exit',
-        filenames=['assert.c', 'atexit.c', 'exit.c'])
+        filenames=['assert.c', 'exit.c'])
     return files
 
   def can_use(self):
@@ -1728,6 +1734,8 @@ def add_library(libname):
 
     if settings.ALLOW_UNIMPLEMENTED_SYSCALLS:
       add_library('libstubs')
+    if not settings.EXIT_RUNTIME:
+      add_library('libnoexit')
     add_library('libc')
     add_library('libcompiler_rt')
     if settings.LINK_AS_CXX: