diff --git a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/FlintSpark.scala b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/FlintSpark.scala
index bfec39f43..fed711368 100644
--- a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/FlintSpark.scala
+++ b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/FlintSpark.scala
@@ -437,9 +437,13 @@ class FlintSpark(val spark: SparkSession) extends Logging {
 
   private def updateIndexAutoToManual(index: FlintSparkIndex): Option[String] = {
     val indexName = index.name
+    // TODO: what if index from api user is not constructed with Builder.copyWithUpdate?
+    val indexLogEntry = index.latestLogEntry.get
     flintClient
       .startTransaction(indexName, dataSourceName)
-      .initialLog(latest => latest.state == REFRESHING)
+      .initialLog(latest =>
+        // TODO: in the future should use another lock to protect entire process and not rely on this
+        latest.state == REFRESHING && latest.seqNo == indexLogEntry.seqNo && latest.primaryTerm == indexLogEntry.primaryTerm)
       .transientLog(latest => latest.copy(state = UPDATING))
       .finalLog(latest => latest.copy(state = ACTIVE))
       .commit(_ => {
@@ -453,10 +457,14 @@ class FlintSpark(val spark: SparkSession) extends Logging {
 
   private def updateIndexManualToAuto(index: FlintSparkIndex): Option[String] = {
     val indexName = index.name
+    // TODO: what if index from api user is not constructed with Builder.copyWithUpdate?
+    val indexLogEntry = index.latestLogEntry.get
     val indexRefresh = FlintSparkIndexRefresh.create(indexName, index)
     flintClient
       .startTransaction(indexName, dataSourceName)
-      .initialLog(latest => latest.state == ACTIVE)
+      .initialLog(latest =>
+        // TODO: in the future should use another lock to protect entire process and not rely on this
+        latest.state == ACTIVE && latest.seqNo == indexLogEntry.seqNo && latest.primaryTerm == indexLogEntry.primaryTerm)
       .transientLog(latest =>
         latest.copy(state = UPDATING, createTime = System.currentTimeMillis()))
       .finalLog(latest => {
diff --git a/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkUpdateIndexITSuite.scala b/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkUpdateIndexITSuite.scala
index 8de8a69be..b475cf95f 100644
--- a/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkUpdateIndexITSuite.scala
+++ b/integ-test/src/test/scala/org/opensearch/flint/spark/FlintSparkUpdateIndexITSuite.scala
@@ -499,28 +499,29 @@ class FlintSparkUpdateIndexITSuite extends FlintSparkSuite {
         .create()
 
       // This update will be delayed
-      val index = flint.describeIndex(testIndex).get
+      val indexInitial = flint.describeIndex(testIndex).get
       val updatedIndexObsolete = flint
         .skippingIndex()
-        .copyWithUpdate(index, FlintSparkIndexOptions(Map("auto_refresh" -> "true", "checkpoint_location" -> checkpointDir.getAbsolutePath)))
+        .copyWithUpdate(indexInitial, FlintSparkIndexOptions(Map("auto_refresh" -> "true", "checkpoint_location" -> checkpointDir.getAbsolutePath)))
 
       // This other update finishes first, converting to auto refresh
       flint.updateIndex(flint
         .skippingIndex()
-        .copyWithUpdate(index, FlintSparkIndexOptions(Map("auto_refresh" -> "true"))))
+        .copyWithUpdate(indexInitial, FlintSparkIndexOptions(Map("auto_refresh" -> "true"))))
       // Adding another update to convert to full refresh, so the obsolete update doesn't fail for option validation or state validation
+      val indexUpdated = flint.describeIndex(testIndex).get
       flint.updateIndex(flint
         .skippingIndex()
-        .copyWithUpdate(index, FlintSparkIndexOptions(Map("auto_refresh" -> "false"))))
+        .copyWithUpdate(indexUpdated, FlintSparkIndexOptions(Map("auto_refresh" -> "false"))))
 
       // This update trying to update an obsolete index should fail
       the[IllegalStateException] thrownBy
         flint.updateIndex(updatedIndexObsolete)
 
       // Verify index after update
-      val readNewIndex = flint.describeIndex(testIndex).get
-      readNewIndex.options.autoRefresh() shouldBe true
-      readNewIndex.options.checkpointLocation() shouldBe empty
+      val indexFinal = flint.describeIndex(testIndex).get
+      indexFinal.options.autoRefresh() shouldBe false
+      indexFinal.options.checkpointLocation() shouldBe empty
     }
   }