diff --git a/src/core/config/commissioner.h b/src/core/config/commissioner.h
index a875d8d23..ff43adb36 100644
--- a/src/core/config/commissioner.h
+++ b/src/core/config/commissioner.h
@@ -55,4 +55,15 @@
 #define OPENTHREAD_CONFIG_COMMISSIONER_MAX_JOINER_ENTRIES 2
 #endif
 
+/**
+ * @def OPENTHREAD_CONFIG_COMMISSIONER_JOINER_SESSION_TIMEOUT
+ *
+ * The timeout for the Joiner's session, in seconds. After this timeout,
+ * the Commissioner tears down the session.
+ *
+ */
+#ifndef OPENTHREAD_CONFIG_COMMISSIONER_JOINER_SESSION_TIMEOUT
+#define OPENTHREAD_CONFIG_COMMISSIONER_JOINER_SESSION_TIMEOUT 30
+#endif
+
 #endif // CONFIG_COMMISSIONER_H_
diff --git a/src/core/meshcop/commissioner.cpp b/src/core/meshcop/commissioner.cpp
index 9c3ecb8ec..be9815314 100644
--- a/src/core/meshcop/commissioner.cpp
+++ b/src/core/meshcop/commissioner.cpp
@@ -66,6 +66,7 @@ Commissioner::Commissioner(Instance &aInstance)
     , mTransmitAttempts(0)
     , mJoinerExpirationTimer(aInstance)
     , mTimer(aInstance)
+    , mJoinerSessionTimer(aInstance)
     , mAnnounceBegin(aInstance)
     , mEnergyScan(aInstance)
     , mPanIdQuery(aInstance)
@@ -137,6 +138,11 @@ void Commissioner::HandleSecureAgentConnected(bool aConnected, void *aContext)
 
 void Commissioner::HandleSecureAgentConnected(bool aConnected)
 {
+    if (!aConnected)
+    {
+        mJoinerSessionTimer.Stop();
+    }
+
     SignalJoinerEvent(aConnected ? kJoinerEventConnected : kJoinerEventEnd, mActiveJoiner);
 }
 
@@ -315,6 +321,7 @@ Error Commissioner::Stop(ResignMode aResignMode)
 
     VerifyOrExit(mState != kStateDisabled, error = kErrorAlready);
 
+    mJoinerSessionTimer.Stop();
     Get<Tmf::SecureAgent>().Stop();
 
     if (mState == kStateActive)
@@ -976,12 +983,20 @@ template <> void Commissioner::HandleTmf<kUriRelayRx>(Coap::Message &aMessage, c
         Get<Tmf::SecureAgent>().SetPsk(joiner->mPskd);
         mActiveJoiner = joiner;
 
+        mJoinerSessionTimer.Start(kJoinerSessionTimeoutMillis);
+
         LogJoinerEntry("Starting new session with", *joiner);
         SignalJoinerEvent(kJoinerEventStart, joiner);
     }
     else
     {
-        VerifyOrExit(mJoinerIid == joinerIid);
+        if (mJoinerIid != joinerIid)
+        {
+            LogNote("Ignore Relay Receive (%s, 0x%04x), session in progress with (%s, 0x%04x)",
+                    joinerIid.ToString().AsCString(), joinerRloc, mJoinerIid.ToString().AsCString(), mJoinerRloc);
+
+            ExitNow();
+        }
     }
 
     mJoinerPort = joinerPort;
@@ -1002,6 +1017,16 @@ exit:
     return;
 }
 
+void Commissioner::HandleJoinerSessionTimer(void)
+{
+    if (mActiveJoiner != nullptr)
+    {
+        LogJoinerEntry("Timed out session with", *mActiveJoiner);
+    }
+
+    Get<Tmf::SecureAgent>().Disconnect();
+}
+
 template <>
 void Commissioner::HandleTmf<kUriDatasetChanged>(Coap::Message &aMessage, const Ip6::MessageInfo &aMessageInfo)
 {
diff --git a/src/core/meshcop/commissioner.hpp b/src/core/meshcop/commissioner.hpp
index c3c4809b2..22e061fb5 100644
--- a/src/core/meshcop/commissioner.hpp
+++ b/src/core/meshcop/commissioner.hpp
@@ -499,6 +499,9 @@ private:
     static constexpr uint32_t kKeepAliveTimeout     = 50; // TIMEOUT_COMM_PET (seconds)
     static constexpr uint32_t kRemoveJoinerDelay    = 20; // Delay to remove successfully joined joiner
 
+    static constexpr uint32_t kJoinerSessionTimeoutMillis =
+        1000 * OPENTHREAD_CONFIG_COMMISSIONER_JOINER_SESSION_TIMEOUT; // Expiration time for active Joiner session
+
     enum ResignMode : uint8_t
     {
         kSendKeepAliveToResign,
@@ -580,6 +583,8 @@ private:
 
     void HandleRelayReceive(Coap::Message &aMessage, const Ip6::MessageInfo &aMessageInfo);
 
+    void HandleJoinerSessionTimer(void);
+
     void SendJoinFinalizeResponse(const Coap::Message &aRequest, StateTlv::State aState);
 
     static Error SendRelayTransmit(void *aContext, Message &aMessage, const Ip6::MessageInfo &aMessageInfo);
@@ -599,6 +604,7 @@ private:
 
     using JoinerExpirationTimer = TimerMilliIn<Commissioner, &Commissioner::HandleJoinerExpirationTimer>;
     using CommissionerTimer     = TimerMilliIn<Commissioner, &Commissioner::HandleTimer>;
+    using JoinerSessionTimer    = TimerMilliIn<Commissioner, &Commissioner::HandleJoinerSessionTimer>;
 
     Joiner mJoiners[OPENTHREAD_CONFIG_COMMISSIONER_MAX_JOINER_ENTRIES];
 
@@ -610,6 +616,7 @@ private:
     uint8_t                  mTransmitAttempts;
     JoinerExpirationTimer    mJoinerExpirationTimer;
     CommissionerTimer        mTimer;
+    JoinerSessionTimer       mJoinerSessionTimer;
 
     AnnounceBeginClient mAnnounceBegin;
     EnergyScanClient    mEnergyScan;