diff --git a/src/core/coap/coap_message.cpp b/src/core/coap/coap_message.cpp
index 41a001dab..3f34b5d71 100644
--- a/src/core/coap/coap_message.cpp
+++ b/src/core/coap/coap_message.cpp
@@ -114,6 +114,16 @@ bool Message::IsNonConfirmablePostRequest(void) const
 
 void Message::Finish(void)
 {
+    // If the payload marker is set but the message contains no
+    // payload, we remove the payload marker from the message. Note
+    // that the presence of a marker followed by a zero-length payload
+    // will be processed as a message format error on the receiver.
+
+    if (GetHelpData().mPayloadMarkerSet && (GetHelpData().mHeaderLength == GetLength()))
+    {
+        IgnoreError(SetLength(GetLength() - 1));
+    }
+
     WriteBytes(0, &GetHelpData().mHeader, GetOptionStart());
 }
 
@@ -330,7 +340,8 @@ Error Message::SetPayloadMarker(void)
 
     VerifyOrExit(GetLength() < kMaxHeaderLength, error = kErrorNoBufs);
     SuccessOrExit(error = Append(marker));
-    GetHelpData().mHeaderLength = GetLength();
+    GetHelpData().mPayloadMarkerSet = true;
+    GetHelpData().mHeaderLength     = GetLength();
 
     // Set offset to the start of payload.
     SetOffset(GetHelpData().mHeaderLength);
diff --git a/src/core/coap/coap_message.hpp b/src/core/coap/coap_message.hpp
index 2fd59da42..305c265ec 100644
--- a/src/core/coap/coap_message.hpp
+++ b/src/core/coap/coap_message.hpp
@@ -42,7 +42,9 @@
 #include "common/code_utils.hpp"
 #include "common/encoding.hpp"
 #include "common/message.hpp"
+#include "net/ip6.hpp"
 #include "net/ip6_address.hpp"
+#include "net/udp6.hpp"
 
 namespace ot {
 
@@ -268,6 +270,9 @@ public:
     /**
      * This method writes header to the message. This must be called before sending the message.
      *
+     * This method also checks whether the payload marker is set (`SetPayloadMarker()`) but the message contains no
+     * payload, and if so it removes the payload marker from the message.
+     *
      */
     void Finish(void);
 
@@ -961,11 +966,16 @@ private:
         uint16_t mOptionLast;
         uint16_t mHeaderOffset; ///< The byte offset for the CoAP Header
         uint16_t mHeaderLength;
+        bool     mPayloadMarkerSet;
 #if OPENTHREAD_CONFIG_COAP_BLOCKWISE_TRANSFER_ENABLE
         BlockWiseData mBlockWiseData;
 #endif
     };
 
+    static_assert(sizeof(HelpData) <= sizeof(Ip6::Header) + sizeof(Ip6::HopByHopHeader) + sizeof(Ip6::OptionMpl) +
+                                          sizeof(Ip6::Udp::Header),
+                  "HelpData size exceeds the size of the reserved region in the message");
+
     const HelpData &GetHelpData(void) const
     {
         static_assert(sizeof(mBuffer.mHead.mMetadata) + sizeof(HelpData) + kHelpDataAlignment <= sizeof(mBuffer),
diff --git a/src/core/meshcop/commissioner.cpp b/src/core/meshcop/commissioner.cpp
index fd2ff640d..87f3c8397 100644
--- a/src/core/meshcop/commissioner.cpp
+++ b/src/core/meshcop/commissioner.cpp
@@ -783,12 +783,6 @@ Error Commissioner::SendMgmtCommissionerSetRequest(const otCommissioningDataset
         SuccessOrExit(error = message->AppendBytes(aTlvs, aLength));
     }
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // no payload, remove coap payload marker
-        IgnoreError(message->SetLength(message->GetLength() - 1));
-    }
-
     messageInfo.SetSockAddr(Get<Mle::MleRouter>().GetMeshLocal16());
     SuccessOrExit(error = Get<Mle::MleRouter>().GetLeaderAloc(messageInfo.GetPeerAddr()));
     messageInfo.SetPeerPort(Tmf::kUdpPort);
diff --git a/src/core/meshcop/dataset_manager.cpp b/src/core/meshcop/dataset_manager.cpp
index 4b0ef40f8..de4adf973 100644
--- a/src/core/meshcop/dataset_manager.cpp
+++ b/src/core/meshcop/dataset_manager.cpp
@@ -442,12 +442,6 @@ void DatasetManager::SendGetResponse(const Coap::Message &   aRequest,
         }
     }
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // no payload, remove coap payload marker
-        IgnoreError(message->SetLength(message->GetLength() - 1));
-    }
-
     SuccessOrExit(error = Get<Tmf::Agent>().SendMessage(*message, aMessageInfo));
 
     otLogInfoMeshCoP("sent %s dataset get response to %s", (GetType() == Dataset::kActive ? "active" : "pending"),
@@ -514,12 +508,6 @@ Error DatasetManager::SendSetRequest(const Dataset::Info &aDatasetInfo, const ui
         SuccessOrExit(error = message->AppendBytes(aTlvs, aLength));
     }
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // no payload, remove coap payload marker
-        IgnoreError(message->SetLength(message->GetLength() - 1));
-    }
-
     messageInfo.SetSockAddr(Get<Mle::MleRouter>().GetMeshLocal16());
     IgnoreError(Get<Mle::MleRouter>().GetLeaderAloc(messageInfo.GetPeerAddr()));
     messageInfo.SetPeerPort(Tmf::kUdpPort);
diff --git a/src/core/thread/network_data_leader_ftd.cpp b/src/core/thread/network_data_leader_ftd.cpp
index 8e5d82f29..60f653536 100644
--- a/src/core/thread/network_data_leader_ftd.cpp
+++ b/src/core/thread/network_data_leader_ftd.cpp
@@ -343,12 +343,6 @@ void Leader::SendCommissioningGetResponse(const Coap::Message &   aRequest,
         }
     }
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // no payload, remove coap payload marker
-        IgnoreError(message->SetLength(message->GetLength() - 1));
-    }
-
     SuccessOrExit(error = Get<Tmf::Agent>().SendMessage(*message, aMessageInfo));
 
     otLogInfoMeshCoP("sent commissioning dataset get response");
diff --git a/src/core/thread/network_diagnostic.cpp b/src/core/thread/network_diagnostic.cpp
index df98a378a..74f7e0c3a 100644
--- a/src/core/thread/network_diagnostic.cpp
+++ b/src/core/thread/network_diagnostic.cpp
@@ -506,12 +506,6 @@ void NetworkDiagnostic::HandleDiagnosticGetQuery(Coap::Message &aMessage, const
 
     SuccessOrExit(error = FillRequestedTlvs(aMessage, *message, networkDiagnosticTlv));
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // Remove Payload Marker if payload is actually empty.
-        IgnoreError(message->SetLength(message->GetLength() - 1));
-    }
-
     SuccessOrExit(error = Get<Tmf::Agent>().SendMessage(*message, messageInfo, nullptr, this));
 
     otLogInfoNetDiag("Sent diagnostic get answer");
@@ -550,12 +544,6 @@ void NetworkDiagnostic::HandleDiagnosticGetRequest(Coap::Message &aMessage, cons
 
     SuccessOrExit(error = FillRequestedTlvs(aMessage, *message, networkDiagnosticTlv));
 
-    if (message->GetLength() == message->GetOffset())
-    {
-        // Remove Payload Marker if payload is actually empty.
-        IgnoreError(message->SetLength(message->GetOffset() - 1));
-    }
-
     SuccessOrExit(error = Get<Tmf::Agent>().SendMessage(*message, messageInfo));
 
     otLogInfoNetDiag("Sent diagnostic get response");