diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/ManifestFileCommitProtocol.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/ManifestFileCommitProtocol.scala
index f6cc8116c6..be7973b9d9 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/ManifestFileCommitProtocol.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/ManifestFileCommitProtocol.scala
@@ -22,7 +22,7 @@ import java.util.UUID
 
 import scala.collection.mutable.ArrayBuffer
 
-import org.apache.hadoop.fs.Path
+import org.apache.hadoop.fs.{FileSystem, Path}
 import org.apache.hadoop.mapreduce.{JobContext, TaskAttemptContext}
 
 import org.apache.spark.internal.Logging
@@ -89,9 +89,7 @@ class ManifestFileCommitProtocol(jobId: String, path: String)
         try {
           val fs = path.getFileSystem(jobContext.getConfiguration)
           // this is to make sure the file can be seen from driver as well
-          if (fs.exists(path)) {
-            fs.delete(path, false)
-          }
+          deleteIfExists(fs, path)
         } catch {
           case e: IOException =>
             logWarning(s"Fail to remove temporary file $path, continue removing next.", e)
@@ -139,7 +137,14 @@ class ManifestFileCommitProtocol(jobId: String, path: String)
     if (addedFiles.nonEmpty) {
       val fs = new Path(addedFiles.head).getFileSystem(taskContext.getConfiguration)
       val statuses: Seq[SinkFileStatus] =
-        addedFiles.map(f => SinkFileStatus(fs.getFileStatus(new Path(f))))
+        addedFiles.flatMap { f =>
+          val path = new Path(f)
+          if (fs.exists(path)) {
+            Some(SinkFileStatus(fs.getFileStatus(path)))
+          } else {
+            None
+          }
+        }
       new TaskCommitMessage(statuses)
     } else {
       new TaskCommitMessage(Seq.empty[SinkFileStatus])
@@ -150,7 +155,13 @@ class ManifestFileCommitProtocol(jobId: String, path: String)
     // best effort cleanup of incomplete files
     if (addedFiles.nonEmpty) {
       val fs = new Path(addedFiles.head).getFileSystem(taskContext.getConfiguration)
-      addedFiles.foreach { file => fs.delete(new Path(file), false) }
+      addedFiles.foreach { file => deleteIfExists(fs, new Path(file)) }
+    }
+  }
+
+  private def deleteIfExists(fs: FileSystem, path: Path, recursive: Boolean = false): Unit = {
+    if (fs.exists(path)) {
+      fs.delete(path, recursive)
     }
   }
 }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/streaming/FileStreamSinkSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/streaming/FileStreamSinkSuite.scala
index 0b885c8429..f04da8bfc4 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/streaming/FileStreamSinkSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/streaming/FileStreamSinkSuite.scala
@@ -600,11 +600,61 @@ class FileStreamSinkV1Suite extends FileStreamSinkSuite {
 }
 
 class FileStreamSinkV2Suite extends FileStreamSinkSuite {
+  import testImplicits._
+
   override protected def sparkConf: SparkConf =
     super
       .sparkConf
       .set(SQLConf.USE_V1_SOURCE_LIST, "")
 
+  test("SPARK-29999 Handle FileStreamSink metadata correctly for empty partition") {
+    Seq("parquet", "orc", "text", "json").foreach { format =>
+      val inputData = MemoryStream[String]
+      val df = inputData.toDF()
+
+      withTempDir { outputDir =>
+        withTempDir { checkpointDir =>
+          var query: StreamingQuery = null
+          try {
+            // repartition to more than the input to leave empty partitions
+            query =
+              df.repartition(10)
+                .writeStream
+                .option("checkpointLocation", checkpointDir.getCanonicalPath)
+                .format(format)
+                .start(outputDir.getCanonicalPath)
+
+            inputData.addData("1", "2", "3")
+            inputData.addData("4", "5")
+
+            failAfter(streamingTimeout) {
+              query.processAllAvailable()
+            }
+          } finally {
+            if (query != null) {
+              query.stop()
+            }
+          }
+
+          val fs = new Path(outputDir.getCanonicalPath).getFileSystem(
+            spark.sessionState.newHadoopConf())
+          val sinkLog = new FileStreamSinkLog(FileStreamSinkLog.VERSION, spark,
+            outputDir.getCanonicalPath)
+
+          val allFiles = sinkLog.allFiles()
+          // only files from non-empty partition should be logged
+          assert(allFiles.length < 10)
+          assert(allFiles.forall(file => fs.exists(new Path(file.path))))
+
+          // the query should be able to read all rows correctly with metadata log
+          val outputDf = spark.read.format(format).load(outputDir.getCanonicalPath)
+            .selectExpr("CAST(value AS INT)").as[Int]
+          checkDatasetUnorderly(outputDf, 1, 2, 3, 4, 5)
+        }
+      }
+    }
+  }
+
   override def checkQueryExecution(df: DataFrame): Unit = {
     // Verify that MetadataLogFileIndex is being used and the correct partitioning schema has
     // been inferred