diff --git a/src/library_dylink.js b/src/library_dylink.js
index 55c40d6f05e99..011b2e569fe7e 100644
--- a/src/library_dylink.js
+++ b/src/library_dylink.js
@@ -588,6 +588,11 @@ var LibraryDylink = {
         }
 #if STACK_OVERFLOW_CHECK >= 2
         if (moduleExports['__set_stack_limits']) {
+#if USE_PTHREADS
+          // When we are on an uninitialized pthread we delay calling
+          // __set_stack_limits until $setDylinkStackLimits.
+          if (!ENVIRONMENT_IS_PTHREAD || runtimeInitialized)
+#endif
           moduleExports['__set_stack_limits'](_emscripten_stack_get_base(), _emscripten_stack_get_end())
         }
 #endif
@@ -646,7 +651,12 @@ var LibraryDylink = {
     return loadModule();
   },
 
-#if STACK_OVERFLOW_CHECK >= 2
+#if STACK_OVERFLOW_CHECK >= 2 && USE_PTHREADS
+  // With USE_PTHREADS we load libraries before we are running a pthread and
+  // therefore before we have a stack.  Instead we delay calling
+  // `__set_stack_limits` until we start running a thread.  We also need to call
+  // this again for each new thread that the runs on a worker (since each thread
+  // has its own separate stack region).
   $setDylinkStackLimits: function(stackTop, stackMax) {
     for (var name in LDSO.loadedLibsByName) {
 #if DYLINK_DEBUG
diff --git a/src/postamble.js b/src/postamble.js
index db52bd790b9f9..b8194b95bca89 100644
--- a/src/postamble.js
+++ b/src/postamble.js
@@ -214,12 +214,16 @@ function stackCheckInit() {
   // This is normally called automatically during __wasm_call_ctors but need to
   // get these values before even running any of the ctors so we call it redundantly
   // here.
-  // TODO(sbc): Move writeStackCookie to native to to avoid this.
+#if ASSERTIONS && USE_PTHREADS
+  // See $establishStackSpace for the equivelent code that runs on a thread
+  assert(!ENVIRONMENT_IS_PTHREAD);
+#endif
 #if RELOCATABLE
   _emscripten_stack_set_limits({{{ STACK_BASE }}} , {{{ STACK_MAX }}});
 #else
   _emscripten_stack_init();
 #endif
+  // TODO(sbc): Move writeStackCookie to native to to avoid this.
   writeStackCookie();
 }
 #endif
@@ -240,7 +244,10 @@ function run(args) {
   }
 
 #if STACK_OVERFLOW_CHECK
-  stackCheckInit();
+#if USE_PTHREADS
+  if (!ENVIRONMENT_IS_PTHREAD)
+#endif
+    stackCheckInit();
 #endif
 
 #if RELOCATABLE
diff --git a/src/preamble.js b/src/preamble.js
index f85d92f4e3e8d..a549455e6f93e 100644
--- a/src/preamble.js
+++ b/src/preamble.js
@@ -375,9 +375,6 @@ function preRun() {
 }
 
 function initRuntime() {
-#if STACK_OVERFLOW_CHECK
-  checkStackCookie();
-#endif
 #if ASSERTIONS
   assert(!runtimeInitialized);
 #endif
@@ -391,6 +388,10 @@ function initRuntime() {
   if (ENVIRONMENT_IS_PTHREAD) return;
 #endif
 
+#if STACK_OVERFLOW_CHECK
+  checkStackCookie();
+#endif
+
 #if STACK_OVERFLOW_CHECK >= 2
 #if RUNTIME_LOGGING
   err('__set_stack_limits: ' + _emscripten_stack_get_base() + ', ' + _emscripten_stack_get_end());
diff --git a/src/runtime_stack_check.js b/src/runtime_stack_check.js
index 075ebab341e5a..61b4377edf3ad 100644
--- a/src/runtime_stack_check.js
+++ b/src/runtime_stack_check.js
@@ -8,6 +8,9 @@
 // Initializes the stack cookie. Called at the startup of main and at the startup of each thread in pthreads mode.
 function writeStackCookie() {
   var max = _emscripten_stack_get_end();
+#if RUNTIME_DEBUG
+  err('writeStackCookie: ' + max.toString(16));
+#endif
 #if ASSERTIONS
   assert((max & 3) == 0);
 #endif