diff --git a/scio-core/src/main/scala/com/spotify/scio/values/SCollection.scala b/scio-core/src/main/scala/com/spotify/scio/values/SCollection.scala
index 245818eed9..c3fa33cf9a 100644
--- a/scio-core/src/main/scala/com/spotify/scio/values/SCollection.scala
+++ b/scio-core/src/main/scala/com/spotify/scio/values/SCollection.scala
@@ -382,11 +382,8 @@ sealed trait SCollection[T] extends PCollectionWrapper[T] {
    * @group collection
    */
   def partitionByKey[U](partitionKeys: Set[U])(f: T => U): Map[U, SCollection[T]] = {
-    val partitionKeysIndexed = partitionKeys.toIndexedSeq
-
-    partitionKeysIndexed
-      .zip(partition(partitionKeys.size, (t: T) => partitionKeysIndexed.indexOf(f(t))))
-      .toMap
+    val partitions = partitionKeys.zipWithIndex.toMap
+    partitionKeys.zip(partition(partitionKeys.size, x => partitions(f(x)))).toMap
   }
 
   /**
diff --git a/scio-core/src/test/scala/com/spotify/scio/values/SCollectionTest.scala b/scio-core/src/test/scala/com/spotify/scio/values/SCollectionTest.scala
index 3f1c082869..25664539f2 100644
--- a/scio-core/src/test/scala/com/spotify/scio/values/SCollectionTest.scala
+++ b/scio-core/src/test/scala/com/spotify/scio/values/SCollectionTest.scala
@@ -40,6 +40,7 @@ import scala.jdk.CollectionConverters._
 import com.spotify.scio.coders.{Beam, Coder, MaterializedCoder}
 import com.spotify.scio.options.ScioOptions
 import com.spotify.scio.schemas.Schema
+import org.apache.beam.sdk.Pipeline.PipelineExecutionException
 import org.apache.beam.sdk.coders.{NullableCoder, StringUtf8Coder}
 
 import java.nio.charset.StandardCharsets
@@ -249,6 +250,16 @@ class SCollectionTest extends PipelineSpec {
       m("b") should containInAnyOrder(Seq("b4", "b5"))
       m("c") should containInAnyOrder(Seq("c6"))
     }
+
+    val e = the[PipelineExecutionException] thrownBy {
+      runWithContext { sc =>
+        sc
+          .parallelize(Seq("x"))
+          .partitionByKey(Set("a", "b", "c"))(_.substring(0, 1))
+      }
+    }
+    e.getCause shouldBe a[NoSuchElementException]
+    e.getCause.getMessage shouldBe "key not found: x"
   }
 
   it should "support hashPartition() based on Object.hashCode()" in {