diff --git a/mllib/src/main/scala/org/apache/spark/ml/feature/StringIndexer.scala b/mllib/src/main/scala/org/apache/spark/ml/feature/StringIndexer.scala
index bfb78adfd42d0..d166b3d3ade4b 100644
--- a/mllib/src/main/scala/org/apache/spark/ml/feature/StringIndexer.scala
+++ b/mllib/src/main/scala/org/apache/spark/ml/feature/StringIndexer.scala
@@ -339,55 +339,40 @@ class StringIndexerModel (
   @Since("3.0.0")
   def setOutputCols(value: Array[String]): this.type = set(outputCols, value)
 
-  // This filters out any null values and also the input labels which are not in
-  // the dataset used for fitting.
-  private def filterInvalidData(
-      dataset: Dataset[_],
-      inputColNames: Seq[String],
-      labelsToIndexArray: Array[OpenHashMap[String, Double]]): Dataset[_] = {
-    val conditions: Seq[Column] = inputColNames.indices.map { i =>
-      val inputColName = inputColNames(i)
-      val labelToIndex = labelsToIndexArray(i)
-      // We have this additional lookup at `labelToIndex` when `handleInvalid` is set to
-      // `StringIndexer.SKIP_INVALID`. Another idea is to do this lookup natively by SQL
-      // expression, however, lookup for a key in a map is not efficient in SparkSQL now.
-      // See `ElementAt` and `GetMapValue` expressions. If SQL's map lookup is improved,
-      // we can consider to change this.
-      val filter = udf { label: String =>
-        labelToIndex.contains(label)
-      }
-      filter(dataset(inputColName))
-    }
-
-    dataset.na.drop(inputColNames.filter(dataset.schema.fieldNames.contains(_)))
-      .where(conditions.reduce(_ and _))
-  }
-
   private def getIndexer(
       labels: Seq[String],
       labelToIndex: OpenHashMap[String, Double],
-      keepInvalid: Boolean) = {
-    val unknownIndex = labels.length.toDouble
-    if (keepInvalid) {
-      udf { label: String =>
-        if (label == null) {
-          unknownIndex
-        } else {
-          labelToIndex.get(label).getOrElse(unknownIndex)
-        }
-      }.asNondeterministic()
-    } else {
-      udf { label: String =>
-        if (label == null) {
-          throw new SparkException("StringIndexer encountered NULL value. To handle or skip " +
-            "NULLS, try setting StringIndexer.handleInvalid.")
-        } else {
-          labelToIndex.get(label).getOrElse {
-            throw new SparkException(s"Unseen label: $label. To handle unseen labels, " +
-              s"set Param handleInvalid to ${StringIndexer.KEEP_INVALID}.")
+      handleInvalid: String) = {
+    handleInvalid match {
+      case StringIndexer.KEEP_INVALID =>
+        val unknownIndex = labels.length.toDouble
+        udf { label: String =>
+          if (label == null) {
+            unknownIndex
+          } else {
+            labelToIndex.get(label).getOrElse(unknownIndex)
           }
-        }
-      }.asNondeterministic()
+        }.asNondeterministic()
+      case StringIndexer.SKIP_INVALID =>
+        udf { label: String =>
+          if (label == null) {
+            null
+          } else {
+            labelToIndex.get(label).map(index => java.lang.Double.valueOf(index)).orNull
+          }
+        }.asNondeterministic()
+      case _ =>
+        udf { label: String =>
+          if (label == null) {
+            throw new SparkException("StringIndexer encountered NULL value. To handle or skip " +
+              "NULLS, try setting StringIndexer.handleInvalid.")
+          } else {
+            labelToIndex.get(label).getOrElse {
+              throw new SparkException(s"Unseen label: $label. To handle unseen labels, " +
+                s"set Param handleInvalid to ${StringIndexer.KEEP_INVALID}.")
+            }
+          }
+        }.asNondeterministic()
     }
   }
 
@@ -404,14 +389,6 @@ class StringIndexerModel (
       map
     }
     val outputColumns = new Array[Column](outputColNames.length)
-    val keepInvalid = getHandleInvalid == StringIndexer.KEEP_INVALID
-
-    // Skips invalid rows if `handleInvalid` is set to `StringIndexer.SKIP_INVALID`.
-    val filteredDataset = if (getHandleInvalid == StringIndexer.SKIP_INVALID) {
-      filterInvalidData(dataset, inputColNames.toImmutableArraySeq, labelsToIndexArray)
-    } else {
-      dataset
-    }
 
     for (i <- outputColNames.indices) {
       val inputColName = inputColNames(i)
@@ -421,13 +398,17 @@ class StringIndexerModel (
 
       try {
         dataset.col(inputColName)
-        val filteredLabels = if (keepInvalid) labels :+ "__unknown" else labels
+        val filteredLabels = if (getHandleInvalid == StringIndexer.KEEP_INVALID) {
+          labels :+ "__unknown"
+        } else {
+          labels
+        }
         val metadata = NominalAttribute.defaultAttr
           .withName(outputColName)
           .withValues(filteredLabels)
           .toMetadata()
 
-        val indexer = getIndexer(labels.toImmutableArraySeq, labelToIndex, keepInvalid)
+        val indexer = getIndexer(labels.toImmutableArraySeq, labelToIndex, getHandleInvalid)
 
         outputColumns(i) = indexer(dataset(inputColName).cast(StringType))
           .as(outputColName, metadata)
@@ -443,10 +424,17 @@ class StringIndexerModel (
 
     require(filteredOutputColNames.length == filteredOutputColumns.length)
     if (filteredOutputColNames.length > 0) {
-      filteredDataset.withColumns(
+      val transformedDataset = dataset.withColumns(
         filteredOutputColNames.toImmutableArraySeq, filteredOutputColumns.toImmutableArraySeq)
+      if (getHandleInvalid == StringIndexer.SKIP_INVALID) {
+        // The skip indexers return null for invalid labels. Their nondeterminism keeps this filter
+        // above the projection, so each label is looked up only once.
+        transformedDataset.na.drop(filteredOutputColNames)
+      } else {
+        transformedDataset
+      }
     } else {
-      filteredDataset.toDF()
+      dataset.toDF()
     }
   }
 
diff --git a/mllib/src/test/scala/org/apache/spark/ml/feature/StringIndexerSuite.scala b/mllib/src/test/scala/org/apache/spark/ml/feature/StringIndexerSuite.scala
index 18005687f5656..01b53993e9f01 100644
--- a/mllib/src/test/scala/org/apache/spark/ml/feature/StringIndexerSuite.scala
+++ b/mllib/src/test/scala/org/apache/spark/ml/feature/StringIndexerSuite.scala
@@ -519,6 +519,26 @@ class StringIndexerSuite extends MLTest with DefaultReadWriteTest {
     }
   }
 
+  test("StringIndexer skips rows with invalid multiple input columns") {
+    val training = Seq(("a", "e"), ("b", "f")).toDF("label1", "label2")
+    val data = Seq(
+      (0, "a", "e"),
+      (1, "c", "e"),
+      (2, "a", "g"),
+      (3, null, "e"),
+      (4, "b", "f")
+    ).toDF("id", "label1", "label2")
+
+    val model = new StringIndexer()
+      .setInputCols(Array("label1", "label2"))
+      .setOutputCols(Array("labelIndex1", "labelIndex2"))
+      .setHandleInvalid("skip")
+      .fit(training)
+
+    val transformed = model.transform(data).select("id", "labelIndex1", "labelIndex2")
+    checkAnswer(transformed, Seq(Row(0, 0.0, 0.0), Row(4, 1.0, 1.0)))
+  }
+
   test("Correctly skipping NULL and NaN values") {
     val df = Seq(("a", Double.NaN), (null, 1.0), ("b", 2.0), (null, 3.0)).toDF("str", "double")