diff --git a/src/messaging/ExchangeContext.cpp b/src/messaging/ExchangeContext.cpp
index d786877c51d0cc..5a183272d719df 100644
--- a/src/messaging/ExchangeContext.cpp
+++ b/src/messaging/ExchangeContext.cpp
@@ -35,6 +35,7 @@
 #include <core/CHIPCore.h>
 #include <core/CHIPEncoding.h>
 #include <core/CHIPKeyIds.h>
+#include <lib/support/TypeTraits.h>
 #include <messaging/ExchangeContext.h>
 #include <messaging/ExchangeMgr.h>
 #include <protocols/Protocols.h>
@@ -79,8 +80,13 @@ void ExchangeContext::SetResponseTimeout(Timeout timeout)
 CHIP_ERROR ExchangeContext::SendMessage(Protocols::Id protocolId, uint8_t msgType, PacketBufferHandle && msgBuf,
                                         const SendFlags & sendFlags)
 {
-    // If we were waiting for a message send, this is it.
-    mFlags.Clear(Flags::kFlagWillSendMessage);
+    if (protocolId != Protocols::SecureChannel::Id || msgType != to_underlying(Protocols::SecureChannel::MsgType::StandaloneAck))
+    {
+        // If we were waiting for a message send, this is it.  Standalone acks
+        // are not application-level sends, which is why we don't allow those to
+        // clear the WillSendMessage flag.
+        mFlags.Clear(Flags::kFlagWillSendMessage);
+    }
 
     CHIP_ERROR err                         = CHIP_NO_ERROR;
     Transport::PeerConnectionState * state = nullptr;
diff --git a/src/protocols/Protocols.h b/src/protocols/Protocols.h
index deeec5b4e6aae4..1cc93f6a7d1b79 100644
--- a/src/protocols/Protocols.h
+++ b/src/protocols/Protocols.h
@@ -42,6 +42,8 @@ class Id
         return mVendorId == aOther.mVendorId && mProtocolId == aOther.mProtocolId;
     }
 
+    constexpr bool operator!=(const Id & aOther) const { return !(*this == aOther); }
+
     // Convert the Protocols::Id to a TLV profile id.
     // NOTE: We may want to change the TLV reader/writer to take Protocols::Id
     // directly later on and get rid of this method.