diff --git a/runtime/vm/base_isolate.h b/runtime/vm/base_isolate.h
index 58a0cbbb8e1..be59b1667c8 100644
--- a/runtime/vm/base_isolate.h
+++ b/runtime/vm/base_isolate.h
@@ -31,13 +31,29 @@ class BaseIsolate {
 #endif
 
  protected:
-  BaseIsolate() : scheduled_mutator_thread_(NULL) {}
+  BaseIsolate() {}
 
   ~BaseIsolate() {
     // Do not delete stack resources: top_resource_ and current_zone_.
   }
 
-  Thread* scheduled_mutator_thread_;
+  Thread* scheduled_mutator_thread_ = nullptr;
+
+  // TODO(asiva): Currently we treat a mutator thread as a special thread
+  // and always schedule execution of Dart code on the same mutator thread
+  // object. The ApiLocalScope has been made thread specific but we still
+  // have scenarios where we do a temporary exit of an Isolate with live
+  // zones/handles in the API scope :
+  // - Dart_RunLoop()
+  // - IsolateSaver in Dart_NewNativePort
+  // Similarly, tracking async_stack_trace requires that we always reschedule
+  // on the same thread.
+  // We probably need a mechanism to return to the specific thread only
+  // for these specific cases. We should also determine if the embedder
+  // should allow exiting an isolate with live state in zones/handles in
+  // which case a new API for returning to the specific thread needs to be
+  // added.
+  Thread* mutator_thread_ = nullptr;
 
  private:
   DISALLOW_COPY_AND_ASSIGN(BaseIsolate);
diff --git a/runtime/vm/compiler/runtime_offsets_extracted.h b/runtime/vm/compiler/runtime_offsets_extracted.h
index dc10a412687..c9d3300fcdb 100644
--- a/runtime/vm/compiler/runtime_offsets_extracted.h
+++ b/runtime/vm/compiler/runtime_offsets_extracted.h
@@ -138,13 +138,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 20;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 28;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 16;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 32;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 16;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 20;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 24;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 28;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 52;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 12;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 36;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 20;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 28;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 32;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 56;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 16;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 16;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 24;
@@ -491,13 +491,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 40;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 52;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 32;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 64;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 32;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 40;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 48;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 56;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 104;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 72;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 40;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 48;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 56;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 64;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 112;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 32;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 32;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 48;
@@ -845,13 +845,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 20;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 28;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 16;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 32;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 16;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 20;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 24;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 28;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 52;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 12;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 36;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 20;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 28;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 32;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 56;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 16;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 16;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 24;
@@ -1194,13 +1194,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 40;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 52;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 32;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 64;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 32;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 40;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 48;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 56;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 104;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 72;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 40;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 48;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 56;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 64;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 112;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 32;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 32;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 48;
@@ -1551,13 +1551,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 40;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 52;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 32;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 64;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 32;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 40;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 48;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 56;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 104;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 72;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 40;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 48;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 56;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 64;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 112;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 32;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 32;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 48;
@@ -1835,13 +1835,13 @@ static constexpr dart::compiler::target::word ICData_owner_offset = 20;
 static constexpr dart::compiler::target::word ICData_state_bits_offset = 28;
 static constexpr dart::compiler::target::word
     ICData_receivers_static_type_offset = 16;
-static constexpr dart::compiler::target::word Isolate_class_table_offset = 32;
-static constexpr dart::compiler::target::word Isolate_current_tag_offset = 16;
-static constexpr dart::compiler::target::word Isolate_default_tag_offset = 20;
-static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 24;
-static constexpr dart::compiler::target::word Isolate_object_store_offset = 28;
-static constexpr dart::compiler::target::word Isolate_single_step_offset = 52;
-static constexpr dart::compiler::target::word Isolate_user_tag_offset = 12;
+static constexpr dart::compiler::target::word Isolate_class_table_offset = 36;
+static constexpr dart::compiler::target::word Isolate_current_tag_offset = 20;
+static constexpr dart::compiler::target::word Isolate_default_tag_offset = 24;
+static constexpr dart::compiler::target::word Isolate_ic_miss_code_offset = 28;
+static constexpr dart::compiler::target::word Isolate_object_store_offset = 32;
+static constexpr dart::compiler::target::word Isolate_single_step_offset = 56;
+static constexpr dart::compiler::target::word Isolate_user_tag_offset = 16;
 static constexpr dart::compiler::target::word LinkedHashMap_data_offset = 16;
 static constexpr dart::compiler::target::word
     LinkedHashMap_deleted_keys_offset = 24;
diff --git a/runtime/vm/isolate.cc b/runtime/vm/isolate.cc
index 52119b78dec..21ba0679279 100644
--- a/runtime/vm/isolate.cc
+++ b/runtime/vm/isolate.cc
@@ -1021,6 +1021,13 @@ Isolate::~Isolate() {
          nullptr);  // No deopt in progress when isolate deleted.
   ASSERT(spawn_count_ == 0);
   delete safepoint_handler_;
+
+  // We have cached the mutator thread, delete it.
+  ASSERT(scheduled_mutator_thread_ == nullptr);
+  mutator_thread_->isolate_ = nullptr;
+  delete mutator_thread_;
+  mutator_thread_ = nullptr;
+
   delete thread_registry_;
 
   if (obfuscation_map_ != nullptr) {
@@ -1177,7 +1184,7 @@ void Isolate::RetainKernelBlob(const ExternalTypedData& kernel_blob) {
 
 Thread* Isolate::mutator_thread() const {
   ASSERT(thread_registry() != nullptr);
-  return thread_registry()->mutator_thread();
+  return mutator_thread_;
 }
 
 RawObject* Isolate::CallTagHandler(Dart_LibraryTag tag,
@@ -2051,6 +2058,12 @@ void Isolate::VisitStackPointers(ObjectPointerVisitor* visitor,
                                  ValidationPolicy validate_frames) {
   // Visit objects in all threads (e.g., Dart stack, handles in zones).
   thread_registry()->VisitObjectPointers(visitor, validate_frames);
+
+  // Visit mutator thread, even if the isolate isn't entered/scheduled (there
+  // might be live API handles to visit).
+  if (mutator_thread_ != nullptr) {
+    mutator_thread_->VisitObjectPointers(visitor, validate_frames);
+  }
 }
 
 void Isolate::VisitWeakPersistentHandles(HandleVisitor* visitor) {
@@ -2887,8 +2900,25 @@ Thread* Isolate::ScheduleThread(bool is_mutator, bool bypass_safepoint) {
       ml.Wait();
     }
 
-    // Now get a free Thread structure.
-    thread = thread_registry()->GetFreeThreadLocked(this, is_mutator);
+    // NOTE: We cannot just use `Dart::vm_isolate() == this` here, since during
+    // VM startup it might not have been set at this point.
+    const bool is_vm_isolate =
+        Dart::vm_isolate() == nullptr || Dart::vm_isolate() == this;
+
+    if (is_mutator) {
+      if (mutator_thread_ == nullptr) {
+        // Allocate a new [Thread] structure for the mutator thread.
+        thread = thread_registry()->GetFreeThreadLocked(is_vm_isolate);
+        mutator_thread_ = thread;
+      } else {
+        // Reuse the existing cached [Thread] structure for the mutator thread.,
+        // see comment in 'base_isolate.h'.
+        thread_registry()->AddToActiveListLocked(mutator_thread_);
+        thread = mutator_thread_;
+      }
+    } else {
+      thread = thread_registry()->GetFreeThreadLocked(is_vm_isolate);
+    }
     ASSERT(thread != nullptr);
 
     thread->ResetHighWatermark();
@@ -2945,9 +2975,7 @@ void Isolate::UnscheduleThread(Thread* thread,
   os_thread->DisableThreadInterrupts();
   os_thread->set_thread(nullptr);
   OSThread::SetCurrent(os_thread);
-  if (is_mutator) {
-    scheduled_mutator_thread_ = nullptr;
-  }
+
   // Even if we unschedule the mutator thread, e.g. via calling
   // `Dart_ExitIsolate()` inside a native, we might still have one or more Dart
   // stacks active, which e.g. GC marker threads want to visit.  So we don't
@@ -2967,8 +2995,16 @@ void Isolate::UnscheduleThread(Thread* thread,
   thread->set_safepoint_state(Thread::SetAtSafepoint(true, 0));
   thread->clear_pending_functions();
   ASSERT(thread->no_safepoint_scope_depth() == 0);
-  // Return thread structure.
-  thread_registry()->ReturnThreadLocked(is_mutator, thread);
+
+  if (is_mutator) {
+    ASSERT(mutator_thread_ == thread);
+    ASSERT(mutator_thread_ == scheduled_mutator_thread_);
+    thread_registry()->RemoveFromActiveListLocked(thread);
+    scheduled_mutator_thread_ = nullptr;
+  } else {
+    // Return thread structure.
+    thread_registry()->ReturnThreadLocked(thread);
+  }
 }
 
 static const char* NewConstChar(const char* chars) {
diff --git a/runtime/vm/thread.cc b/runtime/vm/thread.cc
index 71a9b2d3825..f9bcb736c39 100644
--- a/runtime/vm/thread.cc
+++ b/runtime/vm/thread.cc
@@ -56,7 +56,7 @@ Thread::~Thread() {
 
 #define REUSABLE_HANDLE_INITIALIZERS(object) object##_handle_(NULL),
 
-Thread::Thread(Isolate* isolate)
+Thread::Thread(bool is_vm_isolate)
     : ThreadState(false),
       stack_limit_(0),
       stack_overflow_flags_(0),
@@ -133,7 +133,7 @@ Thread::Thread(Isolate* isolate)
 
   // We cannot initialize the VM constants here for the vm isolate thread
   // due to boot strapping issues.
-  if ((Dart::vm_isolate() != NULL) && (isolate != Dart::vm_isolate())) {
+  if (!is_vm_isolate) {
     InitVMConstants();
   }
 }
diff --git a/runtime/vm/thread.h b/runtime/vm/thread.h
index b13b1490b49..6795aa3744e 100644
--- a/runtime/vm/thread.h
+++ b/runtime/vm/thread.h
@@ -938,7 +938,7 @@ class Thread : public ThreadState {
 
   Thread* next_;  // Used to chain the thread structures in an isolate.
 
-  explicit Thread(Isolate* isolate);
+  explicit Thread(bool is_vm_isolate);
 
   void StoreBufferRelease(
       StoreBuffer::ThresholdPolicy policy = StoreBuffer::kCheckThreshold);
diff --git a/runtime/vm/thread_registry.cc b/runtime/vm/thread_registry.cc
index 2dcabf8234a..6ff47500ea1 100644
--- a/runtime/vm/thread_registry.cc
+++ b/runtime/vm/thread_registry.cc
@@ -4,7 +4,6 @@
 
 #include "vm/thread_registry.h"
 
-#include "vm/isolate.h"
 #include "vm/json_stream.h"
 #include "vm/lockers.h"
 
@@ -17,12 +16,6 @@ ThreadRegistry::~ThreadRegistry() {
     // At this point the active list should be empty.
     ASSERT(active_list_ == NULL);
 
-    // The [mutator_thread_] is kept alive until the destruction of the isolate.
-    mutator_thread_->isolate_ = nullptr;
-
-    // We have cached the mutator thread, delete it.
-    delete mutator_thread_;
-    mutator_thread_ = NULL;
     // Now delete all the threads in the free list.
     while (free_list_ != NULL) {
       Thread* thread = free_list_;
@@ -32,51 +25,34 @@ ThreadRegistry::~ThreadRegistry() {
   }
 }
 
-// Gets a free Thread structure, we special case the mutator thread
-// by reusing the cached structure, see comment in 'thread_registry.h'.
-Thread* ThreadRegistry::GetFreeThreadLocked(Isolate* isolate, bool is_mutator) {
+Thread* ThreadRegistry::GetFreeThreadLocked(bool is_vm_isolate) {
   ASSERT(threads_lock()->IsOwnedByCurrentThread());
-  Thread* thread;
-  if (is_mutator) {
-    if (mutator_thread_ == NULL) {
-      mutator_thread_ = GetFromFreelistLocked(isolate);
-    }
-    thread = mutator_thread_;
-  } else {
-    thread = GetFromFreelistLocked(isolate);
-    ASSERT(thread->api_top_scope() == NULL);
-  }
+  Thread* thread = GetFromFreelistLocked(is_vm_isolate);
+  ASSERT(thread->api_top_scope() == NULL);
   // Now add this Thread to the active list for the isolate.
   AddToActiveListLocked(thread);
   return thread;
 }
 
-void ThreadRegistry::ReturnThreadLocked(bool is_mutator, Thread* thread) {
+void ThreadRegistry::ReturnThreadLocked(Thread* thread) {
   ASSERT(threads_lock()->IsOwnedByCurrentThread());
   // Remove thread from the active list for the isolate.
   RemoveFromActiveListLocked(thread);
-  if (!is_mutator) {
-    ReturnToFreelistLocked(thread);
-  }
+  ReturnToFreelistLocked(thread);
 }
 
 void ThreadRegistry::VisitObjectPointers(ObjectPointerVisitor* visitor,
                                          ValidationPolicy validate_frames) {
   MonitorLocker ml(threads_lock());
-  bool mutator_thread_visited = false;
   Thread* thread = active_list_;
   while (thread != NULL) {
-    thread->VisitObjectPointers(visitor, validate_frames);
-    if (mutator_thread_ == thread) {
-      mutator_thread_visited = true;
+    // The mutator thread is visited by the isolate itself (see
+    // [Isolate::VisitStackPointers]).
+    if (!thread->IsMutatorThread()) {
+      thread->VisitObjectPointers(visitor, validate_frames);
     }
     thread = thread->next_;
   }
-  // Visit mutator thread even if it is not in the active list because of
-  // api handles.
-  if (!mutator_thread_visited && (mutator_thread_ != NULL)) {
-    mutator_thread_->VisitObjectPointers(visitor, validate_frames);
-  }
 }
 
 void ThreadRegistry::ReleaseStoreBuffers() {
@@ -174,12 +150,12 @@ void ThreadRegistry::RemoveFromActiveListLocked(Thread* thread) {
   }
 }
 
-Thread* ThreadRegistry::GetFromFreelistLocked(Isolate* isolate) {
+Thread* ThreadRegistry::GetFromFreelistLocked(bool is_vm_isolate) {
   ASSERT(threads_lock()->IsOwnedByCurrentThread());
   Thread* thread = NULL;
   // Get thread structure from free list or create a new one.
   if (free_list_ == NULL) {
-    thread = new Thread(isolate);
+    thread = new Thread(is_vm_isolate);
   } else {
     thread = free_list_;
     free_list_ = thread->next_;
diff --git a/runtime/vm/thread_registry.h b/runtime/vm/thread_registry.h
index b6c0ec50e75..80f05ca805e 100644
--- a/runtime/vm/thread_registry.h
+++ b/runtime/vm/thread_registry.h
@@ -22,11 +22,7 @@ class JSONArray;
 // Unordered collection of threads relating to a particular isolate.
 class ThreadRegistry {
  public:
-  ThreadRegistry()
-      : threads_lock_(),
-        active_list_(NULL),
-        free_list_(NULL),
-        mutator_thread_(NULL) {}
+  ThreadRegistry() : threads_lock_(), active_list_(NULL), free_list_(NULL) {}
   ~ThreadRegistry();
 
   void VisitObjectPointers(ObjectPointerVisitor* visitor,
@@ -36,8 +32,6 @@ class ThreadRegistry {
   void AcquireMarkingStacks();
   void ReleaseMarkingStacks();
 
-  Thread* mutator_thread() const { return mutator_thread_; }
-
 #ifndef PRODUCT
   void PrintJSON(JSONStream* stream) const;
 #endif
@@ -52,11 +46,11 @@ class ThreadRegistry {
   Thread* active_list() const { return active_list_; }
   Monitor* threads_lock() const { return &threads_lock_; }
 
-  Thread* GetFreeThreadLocked(Isolate* isolate, bool is_mutator);
-  void ReturnThreadLocked(bool is_mutator, Thread* thread);
+  Thread* GetFreeThreadLocked(bool is_vm_isolate);
+  void ReturnThreadLocked(Thread* thread);
   void AddToActiveListLocked(Thread* thread);
   void RemoveFromActiveListLocked(Thread* thread);
-  Thread* GetFromFreelistLocked(Isolate* isolate);
+  Thread* GetFromFreelistLocked(bool is_vm_isolate);
   void ReturnToFreelistLocked(Thread* thread);
 
   // This monitor protects the threads list for an isolate, it is used whenever
@@ -65,22 +59,6 @@ class ThreadRegistry {
   Thread* active_list_;  // List of active threads in the isolate.
   Thread* free_list_;    // Free list of Thread objects that can be reused.
 
-  // TODO(asiva): Currently we treat a mutator thread as a special thread
-  // and always schedule execution of Dart code on the same mutator thread
-  // object. The ApiLocalScope has been made thread specific but we still
-  // have scenarios where we do a temporary exit of an Isolate with live
-  // zones/handles in the API scope :
-  // - Dart_RunLoop()
-  // - IsolateSaver in Dart_NewNativePort
-  // Similarly, tracking async_stack_trace requires that we always reschedule
-  // on the same thread.
-  // We probably need a mechanism to return to the specific thread only
-  // for these specific cases. We should also determine if the embedder
-  // should allow exiting an isolate with live state in zones/handles in
-  // which case a new API for returning to the specific thread needs to be
-  // added.
-  Thread* mutator_thread_;
-
   friend class Isolate;
   friend class SafepointHandler;
   friend class Scavenger;