diff --git a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndex.scala b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndex.scala
index 8e88dd630..c8cb62b2c 100644
--- a/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndex.scala
+++ b/flint-spark-integration/src/main/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndex.scala
@@ -7,6 +7,7 @@ package org.opensearch.flint.spark.covering
 
 import java.util
 
+import org.opensearch.flint.core.metadata.log.FlintMetadataLogEntry.IndexState.DELETED
 import org.opensearch.flint.spark.{FlintSpark, FlintSparkIndex}
 import org.opensearch.flint.spark.covering.FlintSparkCoveringIndex.getFlintIndexName
 
@@ -40,20 +41,18 @@ class ApplyFlintSparkCoveringIndex(flint: FlintSpark) extends Rule[LogicalPlan]
     case relation @ LogicalRelation(_, _, Some(table), false)
         if !plan.isInstanceOf[V2WriteCommand] =>
       val tableName = table.qualifiedName
-      val requiredCols = requiredColumnsInQueryPlan(plan)
+      val requiredCols = collectAllColumnsInQueryPlan(plan)
 
       // Choose the first covering index that meets all criteria above
-      coveringIndexesOnTable(tableName)
+      findAllCoveringIndexesOnTable(tableName)
         .collectFirst {
-          case index: FlintSparkCoveringIndex
-              if index.filterCondition.isEmpty &&
-                requiredCols.subsetOf(index.indexedColumns.keySet) =>
+          case index: FlintSparkCoveringIndex if isCoveringIndexApplicable(index, requiredCols) =>
             replaceTableRelationWithIndexRelation(relation, index)
         }
         .getOrElse(relation) // If no index found, return the original relation
   }
 
-  private def requiredColumnsInQueryPlan(plan: LogicalPlan): Set[String] = {
+  private def collectAllColumnsInQueryPlan(plan: LogicalPlan): Set[String] = {
     // Collect all columns needed by the query, except those in relation. This is because this rule
     // executes before push down optimization and thus relation includes all columns in the table.
     plan
@@ -65,12 +64,20 @@ class ApplyFlintSparkCoveringIndex(flint: FlintSpark) extends Rule[LogicalPlan]
       .toSet
   }
 
-  private def coveringIndexesOnTable(tableName: String): Seq[FlintSparkIndex] = {
+  private def findAllCoveringIndexesOnTable(tableName: String): Seq[FlintSparkIndex] = {
     val qualifiedTableName = qualifyTableName(flint.spark, tableName)
     val indexPattern = getFlintIndexName("*", qualifiedTableName)
     flint.describeIndexes(indexPattern)
   }
 
+  private def isCoveringIndexApplicable(
+      index: FlintSparkCoveringIndex,
+      requiredCols: Set[String]): Boolean = {
+    index.latestLogEntry.exists(_.state != DELETED) &&
+    index.filterCondition.isEmpty &&
+    requiredCols.subsetOf(index.indexedColumns.keySet)
+  }
+
   private def replaceTableRelationWithIndexRelation(
       relation: LogicalRelation,
       index: FlintSparkCoveringIndex): LogicalPlan = {
diff --git a/flint-spark-integration/src/test/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndexSuite.scala b/flint-spark-integration/src/test/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndexSuite.scala
index 5cda20536..6a64be925 100644
--- a/flint-spark-integration/src/test/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndexSuite.scala
+++ b/flint-spark-integration/src/test/scala/org/opensearch/flint/spark/covering/ApplyFlintSparkCoveringIndexSuite.scala
@@ -8,6 +8,8 @@ package org.opensearch.flint.spark.covering
 import org.mockito.ArgumentMatchers.{any, anyString}
 import org.mockito.Mockito.{mockStatic, when, RETURNS_DEEP_STUBS}
 import org.opensearch.flint.core.{FlintClient, FlintClientBuilder, FlintOptions}
+import org.opensearch.flint.core.metadata.log.FlintMetadataLogEntry
+import org.opensearch.flint.core.metadata.log.FlintMetadataLogEntry.IndexState.{ACTIVE, DELETED, IndexState}
 import org.opensearch.flint.spark.FlintSpark
 import org.opensearch.flint.spark.covering.FlintSparkCoveringIndex.getFlintIndexName
 import org.scalatest.matchers.{Matcher, MatchResult}
@@ -51,14 +53,27 @@ class ApplyFlintSparkCoveringIndexSuite extends FlintSuite with Matchers {
     super.afterAll()
   }
 
-  test("should not apply if no index present") {
+  test("should not apply if no covering index present") {
     assertFlintQueryRewriter
       .withQuery(s"SELECT name, age FROM $testTable")
       .assertIndexNotUsed()
   }
 
+  test("should not apply if covering index is logically deleted") {
+    assertFlintQueryRewriter
+      .withQuery(s"SELECT name FROM $testTable")
+      .withIndex(
+        new FlintSparkCoveringIndex(
+          indexName = "name",
+          tableName = testTable,
+          indexedColumns = Map("name" -> "string")),
+        DELETED)
+      .assertIndexNotUsed()
+  }
+
   // Covering index doesn't column age
   Seq(
+    s"SELECT * FROM $testTable",
     s"SELECT name, age FROM $testTable",
     s"SELECT name FROM $testTable WHERE age = 30",
     s"SELECT COUNT(*) FROM $testTable GROUP BY age").foreach { query =>
@@ -78,6 +93,7 @@ class ApplyFlintSparkCoveringIndexSuite extends FlintSuite with Matchers {
   Seq(
     s"SELECT * FROM $testTable",
     s"SELECT name, age FROM $testTable",
+    s"SELECT age, name FROM $testTable",
     s"SELECT name FROM $testTable WHERE age = 30",
     s"SELECT COUNT(*) FROM $testTable GROUP BY age",
     s"SELECT name, COUNT(*) FROM $testTable WHERE age > 30 GROUP BY name").foreach { query =>
@@ -120,8 +136,10 @@ class ApplyFlintSparkCoveringIndexSuite extends FlintSuite with Matchers {
       this
     }
 
-    def withIndex(index: FlintSparkCoveringIndex): AssertionHelper = {
-      this.indexes = indexes :+ index
+    def withIndex(index: FlintSparkCoveringIndex, state: IndexState = ACTIVE): AssertionHelper = {
+      this.indexes = indexes :+
+        index.copy(latestLogEntry =
+          Some(new FlintMetadataLogEntry("id", 0, 0, 0, state, "spark_catalog", "")))
       this
     }