diff --git a/hbase-client/src/main/java/org/apache/hadoop/hbase/client/replication/ReplicationPeerConfigUtil.java b/hbase-client/src/main/java/org/apache/hadoop/hbase/client/replication/ReplicationPeerConfigUtil.java
index 57be558fb492..aafce279e7c6 100644
--- a/hbase-client/src/main/java/org/apache/hadoop/hbase/client/replication/ReplicationPeerConfigUtil.java
+++ b/hbase-client/src/main/java/org/apache/hadoop/hbase/client/replication/ReplicationPeerConfigUtil.java
@@ -458,14 +458,20 @@ public static ReplicationPeerConfig appendTableCFsToReplicationPeerConfig(
   }
 
   /**
-   * Helper method to add/removev base peer configs from Configuration to ReplicationPeerConfig This
-   * merges the user supplied peer configuration
-   * {@link org.apache.hadoop.hbase.replication.ReplicationPeerConfig} with peer configs provided as
-   * property hbase.replication.peer.base.configs in hbase configuration. Expected format for this
-   * hbase configuration is "k1=v1;k2=v2,v2_1;k3=""". If value is empty, it will remove the existing
-   * key-value from peer config.
+   * Helper method to add/remove base peer configs from Configuration to ReplicationPeerConfig.
+   *
+   * Precedence rules:
+   * - If a key exists in both the provided ReplicationPeerConfig and base configs, the value in the
+   *   provided ReplicationPeerConfig is preserved (user-provided wins).
+   * - If a key exists only in base configs (non-empty), it is added to the ReplicationPeerConfig.
+   * - If a key exists in base configs with an empty value (e.g. k1=""), the key is removed from
+   *   the ReplicationPeerConfig.
+   *
+   * The base configs come from the property hbase.replication.peer.base.config in the HBase
+   * configuration. Expected format: "k1=v1;k2=v2,v2_1;k3=\"\"".
+   *
    * @param conf Configuration
-   * @return ReplicationPeerConfig containing updated configs.
+   * @return ReplicationPeerConfig containing updated configs per the precedence rules above.
    */
   public static ReplicationPeerConfig updateReplicationBasePeerConfigs(Configuration conf,
     ReplicationPeerConfig receivedPeerConfig) {
@@ -485,8 +491,8 @@ public static ReplicationPeerConfig updateReplicationBasePeerConfigs(Configurati
         // is required so that it doesn't remove any other config unknowingly.
         if (Strings.isNullOrEmpty(configValue)) {
           copiedPeerConfigBuilder.removeConfiguration(configName);
-        } else if (!receivedPeerConfigMap.getOrDefault(configName, "").equals(configValue)) {
-          // update the configuration if exact config and value doesn't exists
+        } else if (!receivedPeerConfigMap.containsKey(configName)) {
+          // Only add base config if the key is absent in the provided config
           copiedPeerConfigBuilder.putConfiguration(configName, configValue);
         }
       }
diff --git a/hbase-client/src/test/java/org/apache/hadoop/hbase/replication/TestReplicationPeerConfig.java b/hbase-client/src/test/java/org/apache/hadoop/hbase/replication/TestReplicationPeerConfig.java
index bdac27067b09..79b11c18fd44 100644
--- a/hbase-client/src/test/java/org/apache/hadoop/hbase/replication/TestReplicationPeerConfig.java
+++ b/hbase-client/src/test/java/org/apache/hadoop/hbase/replication/TestReplicationPeerConfig.java
@@ -284,21 +284,43 @@ public void testBaseReplicationPeerConfig() throws ReplicationException {
     assertEquals(customPeerConfigSecondValue,
       updatedReplicationPeerConfig.getConfiguration().get(customPeerConfigSecondKey));
 
-    // validates base configs get updated values even if config already present
+    // With new precedence, base updates must NOT override existing keys in peer config
     conf.unset(ReplicationPeerConfigUtil.HBASE_REPLICATION_PEER_BASE_CONFIG);
     conf.set(ReplicationPeerConfigUtil.HBASE_REPLICATION_PEER_BASE_CONFIG,
       customPeerConfigKey.concat("=").concat(customPeerConfigUpdatedValue).concat(";")
-        .concat(customPeerConfigSecondKey).concat("=").concat(customPeerConfigSecondUpdatedValue));
+        .concat(customPeerConfigSecondKey).concat("=")
+        .concat(customPeerConfigSecondUpdatedValue));
 
     ReplicationPeerConfig replicationPeerConfigAfterValueUpdate = ReplicationPeerConfigUtil
       .updateReplicationBasePeerConfigs(conf, updatedReplicationPeerConfig);
 
-    assertEquals(customPeerConfigUpdatedValue,
+    // Expect original values to be preserved since keys already exist in the peer config
+    assertEquals(customPeerConfigValue,
       replicationPeerConfigAfterValueUpdate.getConfiguration().get(customPeerConfigKey));
-    assertEquals(customPeerConfigSecondUpdatedValue,
+    assertEquals(customPeerConfigSecondValue,
       replicationPeerConfigAfterValueUpdate.getConfiguration().get(customPeerConfigSecondKey));
   }
 
+  @Test
+  public void testBaseDoesNotOverrideExistingUserConfig() {
+    String key = "hbase.xxx.override_test";
+    String userValue = "user";
+    String baseValue = "base";
+
+    ReplicationPeerConfig existing = getConfig(1);
+    ReplicationPeerConfig withUser = ReplicationPeerConfig.newBuilder(existing)
+      .putConfiguration(key, userValue).build();
+
+    Configuration conf = new Configuration(CONF);
+    conf.set(ReplicationPeerConfigUtil.HBASE_REPLICATION_PEER_BASE_CONFIG,
+      key.concat("=").concat(baseValue));
+
+    ReplicationPeerConfig merged =
+      ReplicationPeerConfigUtil.updateReplicationBasePeerConfigs(conf, withUser);
+
+    assertEquals(userValue, merged.getConfiguration().get(key));
+  }
+
   @Test
   public void testBaseReplicationRemovePeerConfig() throws ReplicationException {
     String customPeerConfigKey = "hbase.xxx.custom_config";
diff --git a/hbase-server/src/test/java/org/apache/hadoop/hbase/replication/TestMasterReplication.java b/hbase-server/src/test/java/org/apache/hadoop/hbase/replication/TestMasterReplication.java
index 4c0cc89c36df..d6410d41948a 100644
--- a/hbase-server/src/test/java/org/apache/hadoop/hbase/replication/TestMasterReplication.java
+++ b/hbase-server/src/test/java/org/apache/hadoop/hbase/replication/TestMasterReplication.java
@@ -440,8 +440,8 @@ public void testCyclicReplication3() throws Exception {
   }
 
   /**
-   * Tests that base replication peer configs are applied on peer creation and the configs are
-   * overriden if updated as part of updateReplicationPeerConfig()
+   * Tests that base replication peer configs are applied on peer creation and that user-provided
+   * values are preserved on restart when base contains conflicting entries.
    */
   @Test
   public void testBasePeerConfigsForReplicationPeer() throws Exception {
@@ -496,8 +496,8 @@ public void testBasePeerConfigsForReplicationPeer() throws Exception {
       utilities[0].restartHBaseCluster(1);
       admin = utilities[0].getAdmin();
 
-      // Configurations should be updated after restart again
-      Assert.assertEquals(firstCustomPeerConfigValue,
+      // With new precedence, key 1 should retain user override on peer 1; key 2 should be added.
+      Assert.assertEquals(firstCustomPeerConfigUpdatedValue,
         admin.getReplicationPeerConfig("1").getConfiguration().get(firstCustomPeerConfigKey));
       Assert.assertEquals(firstCustomPeerConfigValue,
         admin.getReplicationPeerConfig("2").getConfiguration().get(firstCustomPeerConfigKey));