diff --git a/docs/_plugins/build_api_docs.rb b/docs/_plugins/build_api_docs.rb
index 1ef80bfaf09a4..3072e2ddf85d0 100644
--- a/docs/_plugins/build_api_docs.rb
+++ b/docs/_plugins/build_api_docs.rb
@@ -129,7 +129,9 @@ def build_spark_scala_and_java_docs_if_necessary
     return
   end
 
-  command = "build/sbt -Pkinesis-asl unidoc"
+  # Drop stale genjavadoc trees (target/java) before unifying Javadoc; leftover stubs
+  # (e.g. from a partial or Test/doc run) can make JavaUnidoc fail (SPARK-56827).
+  command = "build/sbt -Pkinesis-asl cleanGenjavadocOutput unidoc"
   puts "Running '#{command}'..."
 
   # Two filter passes on the unidoc output:
diff --git a/project/SparkBuild.scala b/project/SparkBuild.scala
index 66947a58ac590..f471b186e45b0 100644
--- a/project/SparkBuild.scala
+++ b/project/SparkBuild.scala
@@ -1605,6 +1605,11 @@ object Unidoc {
   import sbtunidoc.JavaUnidocPlugin.autoImport._
   import sbtunidoc.ScalaUnidocPlugin.autoImport._
 
+  val cleanGenjavadocOutput = taskKey[Unit](
+    "Delete each module's target/java tree (genjavadoc stubs) before unified API docs " +
+      "so JavaUnidoc cannot pick up stale files (SPARK-56827)."
+  )
+
   protected def ignoreUndocumentedPackages(packages: Seq[Seq[File]]): Seq[Seq[File]] = {
     packages
       .map(_.filterNot(_.getName.contains("$")))
@@ -1729,6 +1734,13 @@ object Unidoc {
       inAnyProject -- inProjects(OldDeps.project, repl, examples, tools, kubernetes,
         yarn, tags, streamingKafka010, sqlKafka010, connectCommon, connect, connectJdbc,
         connectClient, connectShims, protobuf, profiler, udfWorkerProto, udfWorkerCore),
+
+    cleanGenjavadocOutput := {
+      val dirs = target.all(ScopeFilter(inAnyProject)).value
+        .map(_ / "java")
+        .filter(_.isDirectory)
+      IO.delete(dirs)
+    }
   )
 }