diff --git a/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala b/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
index 86807914c2362..557235852fbdb 100644
--- a/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
+++ b/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
@@ -3586,7 +3586,8 @@ object SQLConf {
   val CLASSIC_SHUFFLE_DEPENDENCY_FILE_CLEANUP_ENABLED =
     buildConf("spark.sql.classic.shuffleDependency.fileCleanup.enabled")
       .doc("When enabled, shuffle files will be cleaned up at the end of classic " +
-        "SQL executions.")
+        "SQL executions. Note that this cleanup may cause stage retries and regenerate " +
+        "shuffle files if the same dataframe reference is executed again.")
       .version("4.1.0")
       .booleanConf
       .createWithDefault(Utils.isTesting)
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
index 9f59bded94fe1..6d27740bcea90 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/QueryExecution.scala
@@ -150,7 +150,8 @@ class QueryExecution(
       // with the rest of processing of the root plan being just outputting command results,
       // for eagerly executed commands we mark this place as beginning of execution.
       tracker.setReadyForExecution()
-      val qe = sparkSession.sessionState.executePlan(p, mode)
+      val qe = new QueryExecution(sparkSession, p, mode = mode,
+        shuffleCleanupMode = shuffleCleanupMode)
       val result = QueryExecution.withInternalError(s"Eagerly executed $name failed.") {
         SQLExecution.withNewExecutionId(qe, Some(name)) {
           qe.executedPlan.executeCollect()
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/SQLExecution.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/SQLExecution.scala
index c5c2f9bb6a6f6..1cab0f8d35af5 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/SQLExecution.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/SQLExecution.scala
@@ -30,6 +30,8 @@ import org.apache.spark.internal.config.{SPARK_DRIVER_PREFIX, SPARK_EXECUTOR_PRE
 import org.apache.spark.internal.config.Tests.IS_TESTING
 import org.apache.spark.sql.classic.SparkSession
 import org.apache.spark.sql.execution.adaptive.AdaptiveSparkPlanExec
+import org.apache.spark.sql.execution.command.DataWritingCommandExec
+import org.apache.spark.sql.execution.datasources.v2.V2CommandExec
 import org.apache.spark.sql.execution.exchange.ShuffleExchangeLike
 import org.apache.spark.sql.execution.ui.{SparkListenerSQLExecutionEnd, SparkListenerSQLExecutionStart}
 import org.apache.spark.sql.internal.SQLConf
@@ -68,6 +70,17 @@ object SQLExecution extends Logging {
     }
   }
 
+  private def extractShuffleIds(plan: SparkPlan): Seq[Int] = {
+    plan match {
+      case ae: AdaptiveSparkPlanExec =>
+        ae.context.shuffleIds.asScala.keys.toSeq
+      case nonAdaptivePlan =>
+        nonAdaptivePlan.collect {
+          case exec: ShuffleExchangeLike => exec.shuffleId
+        }
+    }
+  }
+
   /**
    * Wrap an action that will execute "queryExecution" to track all Spark jobs in the body so that
    * we can connect them with an execution.
@@ -177,13 +190,12 @@ object SQLExecution extends Logging {
               if (queryExecution.shuffleCleanupMode != DoNotCleanup
                 && isExecutedPlanAvailable) {
                 val shuffleIds = queryExecution.executedPlan match {
-                  case ae: AdaptiveSparkPlanExec =>
-                    ae.context.shuffleIds.asScala.keys
-                  case nonAdaptivePlan =>
-                    nonAdaptivePlan.collect {
-                      case exec: ShuffleExchangeLike =>
-                        exec.shuffleId
-                    }
+                  case command: V2CommandExec =>
+                    command.children.flatMap(extractShuffleIds)
+                  case dataWritingCommand: DataWritingCommandExec =>
+                    extractShuffleIds(dataWritingCommand.child)
+                  case plan =>
+                    extractShuffleIds(plan)
                 }
                 shuffleIds.foreach { shuffleId =>
                   queryExecution.shuffleCleanupMode match {
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
index a4e4a407255c0..0d0a0f2f31007 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/QueryExecutionSuite.scala
@@ -20,7 +20,7 @@ import scala.collection.mutable
 import scala.io.Source
 import scala.util.Try
 
-import org.apache.spark.sql.{AnalysisException, ExtendedExplainGenerator, FastOperator}
+import org.apache.spark.sql.{AnalysisException, ExtendedExplainGenerator, FastOperator, SaveMode}
 import org.apache.spark.sql.catalyst.{QueryPlanningTracker, QueryPlanningTrackerCallback, TableIdentifier}
 import org.apache.spark.sql.catalyst.analysis.{CurrentNamespace, UnresolvedFunction, UnresolvedRelation}
 import org.apache.spark.sql.catalyst.expressions.{Alias, UnsafeRow}
@@ -327,6 +327,41 @@ class QueryExecutionSuite extends SharedSparkSession {
     }
   }
 
+  test("SPARK-53413: Cleanup shuffle dependencies for commands") {
+    Seq(true, false).foreach { adaptiveEnabled => {
+      withSQLConf((SQLConf.ADAPTIVE_EXECUTION_ENABLED.key, adaptiveEnabled.toString),
+        (SQLConf.CLASSIC_SHUFFLE_DEPENDENCY_FILE_CLEANUP_ENABLED.key, true.toString)) {
+        val plan = spark.range(100).repartition(10).logicalPlan
+        val df = Dataset.ofRows(spark, plan)
+        df.write.format("noop").mode(SaveMode.Overwrite).save()
+
+        val blockManager = spark.sparkContext.env.blockManager
+        assert(blockManager.migratableResolver.getStoredShuffles().isEmpty)
+        assert(blockManager.diskBlockManager.getAllBlocks().isEmpty)
+        }
+      }
+    }
+  }
+
+  test("SPARK-53413: Cleanup shuffle dependencies for DataWritingCommandExec") {
+    withTempDir { dir =>
+      Seq(true, false).foreach { adaptiveEnabled => {
+        withSQLConf((SQLConf.ADAPTIVE_EXECUTION_ENABLED.key, adaptiveEnabled.toString),
+          (SQLConf.CLASSIC_SHUFFLE_DEPENDENCY_FILE_CLEANUP_ENABLED.key, true.toString)) {
+          val plan = spark.range(100).repartition(10).logicalPlan
+          val df = Dataset.ofRows(spark, plan)
+          // V1 API write
+          df.write.format("csv").mode(SaveMode.Overwrite).save(dir.getCanonicalPath)
+
+          val blockManager = spark.sparkContext.env.blockManager
+          assert(blockManager.migratableResolver.getStoredShuffles().isEmpty)
+          assert(blockManager.diskBlockManager.getAllBlocks().isEmpty)
+          }
+        }
+      }
+    }
+  }
+
   test("SPARK-47764: Cleanup shuffle dependencies - DoNotCleanup mode") {
     Seq(true, false).foreach { adaptiveEnabled => {
       withSQLConf((SQLConf.ADAPTIVE_EXECUTION_ENABLED.key, adaptiveEnabled.toString)) {