diff --git a/src/detect-engine-state.c b/src/detect-engine-state.c
index 09815451a539..f62d1472ce3e 100644
--- a/src/detect-engine-state.c
+++ b/src/detect-engine-state.c
@@ -217,17 +217,19 @@ void DetectEngineStateFree(DetectEngineState *state)
  *  \retval 1 inspectable state
  *  \retval 2 inspectable state, but no update
  */
-int DeStateFlowHasInspectableState(Flow *f, AppProto alproto, uint16_t alversion, uint8_t flags)
+int DeStateFlowHasInspectableState(Flow *f, uint8_t alindex, uint16_t alversion, uint8_t flags)
 {
+    AppProto alproto;
     int r = 0;
 
+    alproto =  FlowGetAppProtocolAtIndex(f, alindex);
     SCMutexLock(&f->de_state_m);
     if (f->de_state == NULL || f->de_state->dir_state[flags & STREAM_TOSERVER ? 0 : 1].cnt == 0) {
         if (AppLayerParserProtocolSupportsTxs(f->proto, alproto)) {
             FLOWLOCK_RDLOCK(f);
-            if (FlowGetAppParser(f) != NULL && FlowGetAppState(f) != NULL) {
-                if (AppLayerParserGetTransactionInspectId(FlowGetAppParser(f), flags) >=
-                    AppLayerParserGetTxCnt(f->proto, alproto, FlowGetAppState(f))) {
+            if (FlowGetAppParserAtIndex(f, alindex) != NULL && FlowGetAppStateAtIndex(f, alindex) != NULL) {
+                if (AppLayerParserGetTransactionInspectId(FlowGetAppParserAtIndex(f, alindex), flags) >=
+                    AppLayerParserGetTxCnt(f->proto, alproto, FlowGetAppStateAtIndex(f, alindex))) {
                     r = 2;
                 }
             }
@@ -485,7 +487,7 @@ int DeStateDetectStartDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
 void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
                                     DetectEngineThreadCtx *det_ctx,
                                     Packet *p, Flow *f, uint8_t flags,
-                                    AppProto alproto, uint16_t alversion)
+                                    uint8_t alindex, uint16_t alversion)
 {
     SCMutexLock(&f->de_state_m);
 
@@ -503,6 +505,8 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
     int match = 0;
     uint8_t alert = 0;
 
+    AppProto alproto = FlowGetAppProtocolAtIndex(f, alindex);
+
     DetectEngineStateDirection *dir_state = &f->de_state->dir_state[flags & STREAM_TOSERVER ? 0 : 1];
     DeStateStore *store = dir_state->head;
     void *inspect_tx = NULL;
@@ -519,14 +523,14 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
 
     if (AppLayerParserProtocolSupportsTxs(f->proto, alproto)) {
         FLOWLOCK_RDLOCK(f);
-        alstate = FlowGetAppState(f);
+        alstate = FlowGetAppStateAtIndex(f, alindex);
         if (alstate == NULL) {
             FLOWLOCK_UNLOCK(f);
             SCMutexUnlock(&f->de_state_m);
             return;
         }
 
-        inspect_tx_id = AppLayerParserGetTransactionInspectId(FlowGetAppParser(f),
+        inspect_tx_id = AppLayerParserGetTransactionInspectId(FlowGetAppParserAtIndex(f, alindex),
                                                               flags);
         total_txs = AppLayerParserGetTxCnt(f->proto, alproto, alstate);
         inspect_tx = AppLayerParserGetTx(f->proto, alproto, alstate, inspect_tx_id);
@@ -610,7 +614,7 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
 
             if (alproto_supports_txs) {
                 FLOWLOCK_WRLOCK(f);
-                alstate = FlowGetAppState(f);
+                alstate = FlowGetAppStateAtIndex(f, alindex);
                 if (alstate == NULL) {
                     FLOWLOCK_UNLOCK(f);
                     RULE_PROFILING_END(det_ctx, s, match, p);
@@ -676,7 +680,7 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
                 /* RDLOCK would be nicer, but at least tlsstore needs
                  * write lock currently. */
                 FLOWLOCK_WRLOCK(f);
-                alstate = FlowGetAppState(f);
+                alstate = FlowGetAppStateAtIndex(f, alindex);
                 if (alstate == NULL) {
                     FLOWLOCK_UNLOCK(f);
                     RULE_PROFILING_END(det_ctx, s, 0 /* no match */, p);
@@ -749,7 +753,9 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
     DeStateStoreStateVersion(f->de_state, alversion, flags);
     DeStateStoreFileNoMatchCnt(f->de_state, file_no_match, flags);
 
-    if (!(dir_state->flags & DETECT_ENGINE_STATE_FLAG_FILE_STORE_DISABLED)) {
+    /* Don't enter here if we have a protocol change */
+    if (!(dir_state->flags & DETECT_ENGINE_STATE_FLAG_FILE_STORE_DISABLED) &&
+            (alproto == FlowGetAppProtocol(f))) {
         if (DeStateStoreFilestoreSigsCantMatch(det_ctx->sgh, f->de_state, flags) == 1) {
             SCLogDebug("disabling file storage for transaction");
 
@@ -778,14 +784,14 @@ void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
 /** \brief update flow's inspection id's
  *
  *  \note it is possible that f->alstate, f->alparser are NULL */
-void DeStateUpdateInspectTransactionId(Flow *f, uint8_t direction)
+void DeStateUpdateInspectTransactionId(Flow *f, uint8_t alindex,  uint8_t direction)
 {
     FLOWLOCK_WRLOCK(f);
     if (FlowGetAppParser(f) && FlowGetAppState(f)) {
-        AppLayerParserSetTransactionInspectId(FlowGetAppParser(f),
+        AppLayerParserSetTransactionInspectId(FlowGetAppParserAtIndex(f, alindex),
                                               f->proto,
-                                              FlowGetAppProtocol(f),
-                                              FlowGetAppState(f),
+                                              FlowGetAppProtocolAtIndex(f, alindex),
+                                              FlowGetAppStateAtIndex(f, alindex),
                                               direction);
     }
     FLOWLOCK_UNLOCK(f);
diff --git a/src/detect-engine-state.h b/src/detect-engine-state.h
index 9f497551185f..9135c89aee4b 100644
--- a/src/detect-engine-state.h
+++ b/src/detect-engine-state.h
@@ -151,7 +151,7 @@ void DetectEngineStateFree(DetectEngineState *state);
  * \retval 1 Has state.
  * \retval 0 Has no state.
  */
-int DeStateFlowHasInspectableState(Flow *f, AppProto alproto, uint16_t alversion, uint8_t flags);
+int DeStateFlowHasInspectableState(Flow *f, uint8_t alindex, uint16_t alversion, uint8_t flags);
 
 /**
  * \brief Match app layer sig list against app state and store relevant match
@@ -187,15 +187,16 @@ int DeStateDetectStartDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
 void DeStateDetectContinueDetection(ThreadVars *tv, DetectEngineCtx *de_ctx,
                                     DetectEngineThreadCtx *det_ctx,
                                     Packet *p, Flow *f, uint8_t flags,
-                                    AppProto alproto, uint16_t alversion);
+                                    uint8_t alindex, uint16_t alversion);
 
 /**
  *  \brief Update the inspect id.
  *
  *  \param f Flow(unlocked).
+ *  \param alindex index of applayer to update
  *  \param direction 0 for to server, 1 for toclient.
  */
-void DeStateUpdateInspectTransactionId(Flow *f, uint8_t direction);
+void DeStateUpdateInspectTransactionId(Flow *f, uint8_t alindex,  uint8_t direction);
 
 /**
  * \brief Reset a DetectEngineState state.
diff --git a/src/detect.c b/src/detect.c
index 794ca38ba295..925c7e02eea9 100644
--- a/src/detect.c
+++ b/src/detect.c
@@ -794,8 +794,14 @@ static StreamMsg *SigMatchSignaturesGetSmsg(Flow *f, Packet *p, uint8_t flags)
  */
 static inline void DetectMpmPrefilter(DetectEngineCtx *de_ctx,
         DetectEngineThreadCtx *det_ctx, StreamMsg *smsg, Packet *p,
-        uint8_t flags, AppProto alproto, int has_state, uint8_t *sms_runflags)
+        uint8_t flags, uint8_t alindex, int has_state, uint8_t *sms_runflags)
 {
+    AppProto alproto = ALPROTO_UNKNOWN;
+
+    if (p->flow) {
+        alproto = FlowGetAppProtocolAtIndex(p->flow, alindex);
+    }
+
     /* have a look at the reassembled stream (if any) */
     if (p->flowflags & FLOW_PKT_ESTABLISHED) {
         SCLogDebug("p->flowflags & FLOW_PKT_ESTABLISHED");
@@ -803,7 +809,7 @@ static inline void DetectMpmPrefilter(DetectEngineCtx *de_ctx,
         /* all http based mpms */
         if (has_state && alproto == ALPROTO_HTTP) {
             FLOWLOCK_WRLOCK(p->flow);
-            void *alstate = FlowGetAppState(p->flow);
+            void *alstate = FlowGetAppStateAtIndex(p->flow, alindex);
             if (alstate == NULL) {
                 SCLogDebug("no alstate");
                 FLOWLOCK_UNLOCK(p->flow);
@@ -818,7 +824,7 @@ static inline void DetectMpmPrefilter(DetectEngineCtx *de_ctx,
             }
 
             int tx_progress = 0;
-            uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParser(p->flow),
+            uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParserAtIndex(p->flow, alindex),
                                                                  flags);
             uint64_t total_txs = AppLayerParserGetTxCnt(p->flow->proto, ALPROTO_HTTP, alstate);
             for (; idx < total_txs; idx++) {
@@ -937,14 +943,14 @@ static inline void DetectMpmPrefilter(DetectEngineCtx *de_ctx,
             if (p->flowflags & FLOW_PKT_TOSERVER) {
                 if (det_ctx->sgh->flags & SIG_GROUP_HEAD_MPM_DNSQUERY) {
                     FLOWLOCK_RDLOCK(p->flow);
-                    void *alstate = FlowGetAppState(p->flow);
+                    void *alstate = FlowGetAppStateAtIndex(p->flow, alindex);
                     if (alstate == NULL) {
                         SCLogDebug("no alstate");
                         FLOWLOCK_UNLOCK(p->flow);
                         return;
                     }
 
-                    uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParser(p->flow),
+                    uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParserAtIndex(p->flow, alindex),
                                                                          flags);
                     uint64_t total_txs = AppLayerParserGetTxCnt(p->flow->proto, alproto, alstate);
                     for (; idx < total_txs; idx++) {
@@ -1000,14 +1006,14 @@ static inline void DetectMpmPrefilter(DetectEngineCtx *de_ctx,
             SCLogDebug("mpm inspection");
             if (det_ctx->sgh->flags & SIG_GROUP_HEAD_MPM_DNSQUERY) {
                 FLOWLOCK_RDLOCK(p->flow);
-                void *alstate = FlowGetAppState(p->flow);
+                void *alstate = FlowGetAppStateAtIndex(p->flow, alindex);
                 if (alstate == NULL) {
                     SCLogDebug("no alstate");
                     FLOWLOCK_UNLOCK(p->flow);
                     return;
                 }
 
-                uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParser(p->flow),
+                uint64_t idx = AppLayerParserGetTransactionInspectId(FlowGetAppParserAtIndex(p->flow, alindex),
                                                                      flags);
                 uint64_t total_txs = AppLayerParserGetTxCnt(p->flow->proto, alproto, alstate);
                 for (; idx < total_txs; idx++) {
@@ -1113,6 +1119,7 @@ int SigMatchSignatures(ThreadVars *th_v, DetectEngineCtx *de_ctx, DetectEngineTh
     uint8_t sms_runflags = 0;   /* function flags */
     uint8_t alert_flags = 0;
     AppProto alproto = ALPROTO_UNKNOWN;
+    uint8_t alindex = 0;
 #ifdef PROFILING
     int smatch = 0; /* signature match: 1, no match: 0 */
 #endif
@@ -1210,6 +1217,7 @@ int SigMatchSignatures(ThreadVars *th_v, DetectEngineCtx *de_ctx, DetectEngineTh
             {
                 has_state = (FlowGetAppState(pflow) != NULL);
                 alproto = FlowGetAppProtocol(pflow);
+                alindex = FlowGetAppLayerIndex(pflow);
                 alversion = AppLayerParserGetStateVersion(FlowGetAppParser(pflow));
                 SCLogDebug("alstate %s, alproto %u", has_state ? "true" : "false", alproto);
             } else {
@@ -1307,10 +1315,10 @@ int SigMatchSignatures(ThreadVars *th_v, DetectEngineCtx *de_ctx, DetectEngineTh
     if ((p->flags & PKT_HAS_FLOW) && has_state) {
         /* initialize to 0(DE_STATE_MATCH_HAS_NEW_STATE) */
         memset(det_ctx->de_state_sig_array, 0x00, det_ctx->de_state_sig_array_len);
-        int has_inspectable_state = DeStateFlowHasInspectableState(pflow, alproto, alversion, flags);
+        int has_inspectable_state = DeStateFlowHasInspectableState(pflow, alindex, alversion, flags);
         if (has_inspectable_state == 1) {
             DeStateDetectContinueDetection(th_v, de_ctx, det_ctx, p, pflow,
-                                           flags, alproto, alversion);
+                                           flags, alindex, alversion);
         } else if (has_inspectable_state == 2) {
             /* no inspectable state, so pretend we don't have a state at all */
             has_state = 0;
@@ -1324,7 +1332,7 @@ int SigMatchSignatures(ThreadVars *th_v, DetectEngineCtx *de_ctx, DetectEngineTh
 
     /* run the mpm for each type */
     PACKET_PROFILING_DETECT_START(p, PROF_DETECT_MPM);
-    DetectMpmPrefilter(de_ctx, det_ctx, smsg, p, flags, alproto, has_state, &sms_runflags);
+    DetectMpmPrefilter(de_ctx, det_ctx, smsg, p, flags, alindex, has_state, &sms_runflags);
     PACKET_PROFILING_DETECT_END(p, PROF_DETECT_MPM);
 
     PACKET_PROFILING_DETECT_START(p, PROF_DETECT_PREFILTER);
@@ -1583,7 +1591,7 @@ int SigMatchSignatures(ThreadVars *th_v, DetectEngineCtx *de_ctx, DetectEngineTh
     /* see if we need to increment the inspect_id and reset the de_state */
     if (has_state && AppLayerParserProtocolSupportsTxs(p->proto, alproto)) {
         PACKET_PROFILING_DETECT_START(p, PROF_DETECT_STATEFUL);
-        DeStateUpdateInspectTransactionId(pflow, flags);
+        DeStateUpdateInspectTransactionId(pflow, alindex, flags);
         PACKET_PROFILING_DETECT_END(p, PROF_DETECT_STATEFUL);
     }
 
diff --git a/src/flow.c b/src/flow.c
index 2abd113b9bbf..81c7d90fc5e1 100644
--- a/src/flow.c
+++ b/src/flow.c
@@ -835,21 +835,41 @@ int FlowSetProtoEmergencyTimeout(uint8_t proto, uint32_t emerg_new_timeout,
     return 1;
 }
 
+uint8_t FlowGetAppLayerIndex(const Flow *f)
+{
+    return f->applayer_index;
+}
+
 AppProto FlowGetAppProtocol(const Flow *f)
 {
     return FLOW_GET_CURRENT_APPLAYER(f).alproto;
 }
 
+AppProto FlowGetAppProtocolAtIndex(const Flow *f, uint8_t index)
+{
+    return FLOW_GET_APPLAYER(f, index).alproto;
+}
+
 void *FlowGetAppState(const Flow *f)
 {
     return FLOW_GET_CURRENT_APPLAYER(f).alstate;
 }
 
+void *FlowGetAppStateAtIndex(const Flow *f, uint8_t index)
+{
+    return FLOW_GET_APPLAYER(f, index).alstate;
+}
+
 AppLayerParserState *FlowGetAppParser(const Flow *f)
 {
     return FLOW_GET_CURRENT_APPLAYER(f).alparser;
 }
 
+AppLayerParserState *FlowGetAppParserAtIndex(const Flow *f, uint8_t index)
+{
+    return FLOW_GET_APPLAYER(f, index).alparser;
+}
+
 void FlowSetAppProtocol(Flow *f, AppProto proto)
 {
     FLOW_GET_CURRENT_APPLAYER(f).alproto = proto;
diff --git a/src/flow.h b/src/flow.h
index 55cd158f3d3d..d1b3b3d93526 100644
--- a/src/flow.h
+++ b/src/flow.h
@@ -582,6 +582,10 @@ AppLayerParserState *FlowGetAppParser(const Flow *f);
 void FlowSetAppProtocol(Flow *f, AppProto proto);
 void FlowSetAppState(Flow *f, void *state);
 void FlowSetAppParser(Flow *f, void *parser);
+uint8_t FlowGetAppLayerIndex(const Flow *f);
+AppProto FlowGetAppProtocolAtIndex(const Flow *f, uint8_t index);
+void *FlowGetAppStateAtIndex(const Flow *f, uint8_t index);
+AppLayerParserState *FlowGetAppParserAtIndex(const Flow *f, uint8_t index);