diff --git a/src/counters.c b/src/counters.c
index dd90b2e57f..b375eff4db 100644
--- a/src/counters.c
+++ b/src/counters.c
@@ -468,11 +468,11 @@ static void *SCPerfMgmtThread(void *arg)
         SCPerfOutputCounters();
 
         if (TmThreadsCheckFlag(tv_local, THV_KILL)) {
-            TmThreadsSetFlag(tv_local, THV_CLOSED);
             run = 0;
         }
     }
 
+    TmThreadsSetFlag(tv_local, THV_CLOSED);
     return NULL;
 }
 
diff --git a/src/flow.c b/src/flow.c
index 085d77682f..3f518d85ba 100644
--- a/src/flow.c
+++ b/src/flow.c
@@ -1156,6 +1156,7 @@ void *FlowManagerThread(void *td)
     SCLogInfo("prune_usecnt %"PRIu64, prune_usecnt);
 #endif
 
+    TmThreadsSetFlag(th_v, THV_CLOSED);
     pthread_exit((void *) 0);
 }
 
diff --git a/src/suricata.h b/src/suricata.h
index 8ee6681ac5..d05d35a47d 100644
--- a/src/suricata.h
+++ b/src/suricata.h
@@ -66,6 +66,8 @@ SCDQDataQueue data_queues[256];
 /* memset to zeros, and mutex init! */
 void GlobalInits();
 
+extern uint8_t suricata_ctl_flags;
+
 /* uppercase to lowercase conversion lookup table */
 uint8_t g_u8_lowercasetable[256];
 
diff --git a/src/threadvars.h b/src/threadvars.h
index 31a0627772..c96ad9ed48 100644
--- a/src/threadvars.h
+++ b/src/threadvars.h
@@ -41,7 +41,7 @@ struct TmSlot_;
 #define THV_CLOSED    0x20 /** thread done, should be joinable */
 
 /** Thread flags set and read by threads, to control the threads, when they
-    encounter certain conditions like failure */
+ *  encounter certain conditions like failure */
 #define THV_RESTART_THREAD 0x01 /** restart the thread */
 #define THV_ENGINE_EXIT 0x02 /** shut the engine down gracefully */
 
diff --git a/src/tm-threads.c b/src/tm-threads.c
index b15baf5420..6437a4edd9 100644
--- a/src/tm-threads.c
+++ b/src/tm-threads.c
@@ -1467,12 +1467,17 @@ void TmThreadCheckThreadState(void)
         while (tv) {
             if (TmThreadsCheckFlag(tv, THV_FAILED)) {
                 pthread_join(tv->t, NULL);
-                if ( !(tv_aof & THV_ENGINE_EXIT) &&
-                     (tv->aof & THV_RESTART_THREAD) ) {
-                    TmThreadRestartThread(tv);
-                } else {
-                    TmThreadsSetFlag(tv, THV_CLOSED);
+                if (tv_aof & THV_ENGINE_EXIT || tv->aof & THV_ENGINE_EXIT) {
                     EngineKill();
+                    return;
+                } else {
+                    /* if the engine kill-stop has been received by now, chuck
+                     * restarting and return to kill the engine */
+                    if (suricata_ctl_flags & SURICATA_KILL ||
+                        suricata_ctl_flags & SURICATA_STOP) {
+                        return;
+                    }
+                    TmThreadRestartThread(tv);
                 }
             }
             tv = tv->next;