diff --git a/src/coreclr/debug/ee/controller.cpp b/src/coreclr/debug/ee/controller.cpp
index 47b6e0b5a8134..544bc824aa0e0 100644
--- a/src/coreclr/debug/ee/controller.cpp
+++ b/src/coreclr/debug/ee/controller.cpp
@@ -7585,7 +7585,15 @@ bool DebuggerStepper::TriggerSingleStep(Thread *thread, const BYTE *ip)
     if (!g_pEEInterface->IsManagedNativeCode(ip))
     {
         LOG((LF_CORDB,LL_INFO10000, "DS::TSS: not in managed code, Returning false (case 0)!\n"));
-        DisableSingleStep();
+        // Sometimes we can get here with a callstack that is coming from an APC
+        // this will disable the single stepping and incorrectly resume an app that the user
+        // is stepping through.
+#ifdef FEATURE_THREAD_ACTIVATION        
+        if ((thread->m_State & Thread::TS_DebugWillSync) == 0)
+#endif   
+        {
+            DisableSingleStep();
+        }
         return false;
     }
 
diff --git a/src/coreclr/vm/threadsuspend.cpp b/src/coreclr/vm/threadsuspend.cpp
index 6bc046e2b40bd..505ceb174684f 100644
--- a/src/coreclr/vm/threadsuspend.cpp
+++ b/src/coreclr/vm/threadsuspend.cpp
@@ -5732,8 +5732,9 @@ BOOL CheckActivationSafePoint(SIZE_T ip)
     Thread *pThread = GetThreadNULLOk();
 
     // The criteria for safe activation is to be running managed code.
-    // Also we are not interested in handling interruption if we are already in preemptive mode.
-    BOOL isActivationSafePoint = pThread != NULL &&
+    // Also we are not interested in handling interruption if we are already in preemptive mode nor if we are single stepping
+    BOOL isActivationSafePoint = pThread != NULL && 
+        (pThread->m_StateNC & Thread::TSNC_DebuggerIsStepping) == 0 &&
         pThread->PreemptiveGCDisabled() &&
         ExecutionManager::IsManagedCode(ip);
 
@@ -5918,7 +5919,12 @@ bool Thread::InjectActivation(ActivationReason reason)
     {
         return true;
     }
-
+    // Avoid APC calls when the thread is in single step state to avoid any
+    // wrong resume because it's running a native code.
+    if ((m_StateNC & Thread::TSNC_DebuggerIsStepping) != 0)
+    {
+        return false;
+    }
 #ifdef FEATURE_SPECIAL_USER_MODE_APC
     _ASSERTE(UseSpecialUserModeApc());