diff --git a/common/src/main/scala/org/apache/comet/CometConf.scala b/common/src/main/scala/org/apache/comet/CometConf.scala
index bfe90181ff..a8d2a6762f 100644
--- a/common/src/main/scala/org/apache/comet/CometConf.scala
+++ b/common/src/main/scala/org/apache/comet/CometConf.scala
@@ -262,6 +262,18 @@ object CometConf extends ShimCometConf {
     .booleanConf
     .createWithDefault(true)
 
+  val COMET_EXEC_COVERAGE_THRESHOLD: ConfigEntry[Double] =
+    conf(s"$COMET_EXEC_CONFIG_PREFIX.coverageThreshold")
+      .category(CATEGORY_EXEC)
+      .doc(
+        "Minimum fraction of eligible operators that must be converted to Comet native " +
+          "operators for the native plan to be used. If the coverage is below this threshold, " +
+          "Comet falls back to the original Spark plan. A value of 0.0 disables this check. " +
+          "For example, 0.5 means at least 50% of eligible operators must be Comet-accelerated.")
+      .doubleConf
+      .checkValue(v => v >= 0.0 && v <= 1.0, "Coverage threshold must be between 0.0 and 1.0")
+      .createWithDefault(0.0)
+
   val COMET_EXEC_PROJECT_ENABLED: ConfigEntry[Boolean] =
     createExecEnabledConfig("project", defaultValue = true)
   val COMET_EXEC_FILTER_ENABLED: ConfigEntry[Boolean] =
diff --git a/docs/source/user-guide/latest/tuning.md b/docs/source/user-guide/latest/tuning.md
index 5939e89ef3..fd78480f75 100644
--- a/docs/source/user-guide/latest/tuning.md
+++ b/docs/source/user-guide/latest/tuning.md
@@ -116,6 +116,22 @@ to test with both for your specific workloads.
 
 To configure Comet to convert `SortMergeJoin` to `ShuffledHashJoin`, set `spark.comet.exec.replaceSortMergeJoin=true`.
 
+## Coverage Threshold
+
+When Comet can only accelerate a small fraction of the operators in a query, the overhead from transitions between
+Spark and Comet execution may outweigh the benefit of native execution. The `spark.comet.exec.coverageThreshold`
+configuration allows you to set a minimum coverage percentage. If the fraction of operators that Comet can convert
+falls below this threshold, Comet will fall back to the original Spark plan for the entire query.
+
+For example, to require that at least 50% of eligible operators are converted before using Comet:
+
+```
+spark.comet.exec.coverageThreshold=0.5
+```
+
+The default value is `0.0`, which disables the check and preserves the existing behavior of always using Comet when
+possible. When the threshold is triggered, a warning is logged with the coverage statistics.
+
 ## Shuffle
 
 Comet provides accelerated shuffle implementations that can be used to improve the performance of your queries.
diff --git a/spark/src/main/scala/org/apache/comet/ExtendedExplainInfo.scala b/spark/src/main/scala/org/apache/comet/ExtendedExplainInfo.scala
index f47428e801..6ad163bb4c 100644
--- a/spark/src/main/scala/org/apache/comet/ExtendedExplainInfo.scala
+++ b/spark/src/main/scala/org/apache/comet/ExtendedExplainInfo.scala
@@ -99,18 +99,7 @@ class ExtendedExplainInfo extends ExtendedExplainGenerator {
       outString: StringBuilder,
       planStats: CometCoverageStats): Unit = {
 
-    node match {
-      case _: AdaptiveSparkPlanExec | _: InputAdapter | _: QueryStageExec |
-          _: WholeStageCodegenExec | _: ReusedExchangeExec | _: AQEShuffleReadExec =>
-      // ignore
-      case _: RowToColumnarExec | _: ColumnarToRowExec | _: CometColumnarToRowExec |
-          _: CometNativeColumnarToRowExec | _: CometSparkToColumnarExec =>
-        planStats.transitions += 1
-      case _: CometPlan =>
-        planStats.cometOperators += 1
-      case _ =>
-        planStats.sparkOperators += 1
-    }
+    planStats.classifyNode(node)
 
     outString.append("   " * indent)
     if (depth > 0) {
@@ -182,14 +171,51 @@ class CometCoverageStats {
   var cometOperators: Int = 0
   var transitions: Int = 0
 
+  def eligible: Int = sparkOperators + cometOperators
+
+  def coverageFraction: Double =
+    if (eligible == 0) 0.0 else cometOperators.toDouble / eligible
+
   override def toString(): String = {
-    val eligible = sparkOperators + cometOperators
-    val converted =
-      if (eligible == 0) 0.0 else cometOperators.toDouble / eligible * 100.0
     s"Comet accelerated $cometOperators out of $eligible " +
-      s"eligible operators (${converted.toInt}%). " +
+      s"eligible operators (${(coverageFraction * 100).toInt}%). " +
       s"Final plan contains $transitions transitions between Spark and Comet."
   }
+
+  def classifyNode(node: TreeNode[_]): Unit = {
+    node match {
+      case _: AdaptiveSparkPlanExec | _: InputAdapter | _: QueryStageExec |
+          _: WholeStageCodegenExec | _: ReusedExchangeExec | _: AQEShuffleReadExec =>
+      // ignore
+      case _: RowToColumnarExec | _: ColumnarToRowExec | _: CometColumnarToRowExec |
+          _: CometNativeColumnarToRowExec | _: CometSparkToColumnarExec =>
+        transitions += 1
+      case _: CometPlan =>
+        cometOperators += 1
+      case _ =>
+        sparkOperators += 1
+    }
+  }
+}
+
+object CometCoverageStats {
+  def fromPlan(plan: SparkPlan): CometCoverageStats = {
+    val stats = new CometCoverageStats()
+    collectStats(getActualPlan(plan), stats)
+    stats
+  }
+
+  private def collectStats(node: TreeNode[_], stats: CometCoverageStats): Unit = {
+    stats.classifyNode(node)
+    node.innerChildren.foreach {
+      case c: TreeNode[_] => collectStats(getActualPlan(c), stats)
+      case _ =>
+    }
+    node.children.foreach {
+      case c: TreeNode[_] => collectStats(getActualPlan(c), stats)
+      case _ =>
+    }
+  }
 }
 
 object CometExplainInfo {
diff --git a/spark/src/main/scala/org/apache/comet/rules/CometExecRule.scala b/spark/src/main/scala/org/apache/comet/rules/CometExecRule.scala
index 76e741e3bf..b09a8b8e5c 100644
--- a/spark/src/main/scala/org/apache/comet/rules/CometExecRule.scala
+++ b/spark/src/main/scala/org/apache/comet/rules/CometExecRule.scala
@@ -47,7 +47,7 @@ import org.apache.spark.sql.execution.window.WindowExec
 import org.apache.spark.sql.internal.SQLConf
 import org.apache.spark.sql.types._
 
-import org.apache.comet.{CometConf, CometExplainInfo, ExtendedExplainInfo}
+import org.apache.comet.{CometConf, CometCoverageStats, CometExplainInfo, ExtendedExplainInfo}
 import org.apache.comet.CometConf.{COMET_SPARK_TO_ARROW_ENABLED, COMET_SPARK_TO_ARROW_SUPPORTED_OPERATOR_LIST}
 import org.apache.comet.CometSparkSessionExtensions._
 import org.apache.comet.rules.CometExecRule.allExecs
@@ -444,7 +444,7 @@ case class CometExecRule(session: SparkSession) extends Rule[SparkPlan] {
 
       // Convert native execution block by linking consecutive native operators.
       var firstNativeOp = true
-      newPlan.transformDown {
+      val finalPlan = newPlan.transformDown {
         case op: CometNativeExec =>
           val newPlan = if (firstNativeOp) {
             firstNativeOp = false
@@ -475,6 +475,22 @@ case class CometExecRule(session: SparkSession) extends Rule[SparkPlan] {
           firstNativeOp = true
           op
       }
+
+      // Check coverage threshold - if the fraction of converted operators is too low,
+      // fall back to the original Spark plan.
+      val threshold = CometConf.COMET_EXEC_COVERAGE_THRESHOLD.get(conf)
+      if (threshold > 0.0) {
+        val stats = CometCoverageStats.fromPlan(finalPlan)
+        if (stats.eligible > 0 && stats.coverageFraction < threshold) {
+          logWarning(
+            s"Comet native coverage ${(stats.coverageFraction * 100).toInt}% " +
+              s"is below threshold ${(threshold * 100).toInt}% " +
+              s"($stats). Falling back to Spark plan.")
+          return plan
+        }
+      }
+
+      finalPlan
     }
   }