diff --git a/core/src/main/scala/kafka/log/LogManager.scala b/core/src/main/scala/kafka/log/LogManager.scala
index e420b0df435da..805a8f7e037de 100755
--- a/core/src/main/scala/kafka/log/LogManager.scala
+++ b/core/src/main/scala/kafka/log/LogManager.scala
@@ -270,26 +270,38 @@ class LogManager(logDirs: Seq[File],
   def directoryId(dir: String): Option[Uuid] = dirIds.get(dir)
 
   /**
-   * Determine directory ID for each directory with a meta.properties.
+   * Determine directory ID for each directory.
    * If meta.properties does not include a directory ID, one is generated and persisted back to meta.properties.
-   * Directories without a meta.properties don't get a directory ID assigned.
+   * Directories without a meta.properties file, which can only occur in Zk mode, will file have a directory ID assigned.
+   * The ID will be written when the new meta.properties file is first written.
    */
   private def directoryIds(dirs: Seq[File]): Map[String, Uuid] = {
+    val s = scala.collection.mutable.Set[Uuid]()
     dirs.flatMap { dir =>
       try {
         val metadataCheckpoint = new BrokerMetadataCheckpoint(new File(dir, KafkaServer.brokerMetaPropsFile))
-        metadataCheckpoint.read().map { props =>
-          val rawMetaProperties = new RawMetaProperties(props)
-          val uuid = rawMetaProperties.directoryId match {
-            case Some(uuidStr) => Uuid.fromString(uuidStr)
-            case None =>
-              val uuid = Uuid.randomUuid()
-              rawMetaProperties.directoryId = uuid.toString
-              metadataCheckpoint.write(rawMetaProperties.props)
-              uuid
+        val uuid = metadataCheckpoint.read() match {
+          case Some(props) => {
+            val rawMetaProperties = new RawMetaProperties(props)
+            val uuid_from_properties = rawMetaProperties.directoryId match {
+              case Some(uuidStr) => Uuid.fromString(uuidStr)
+              case None =>
+                val uuid_new = Uuid.randomUuid()
+                rawMetaProperties.directoryId = uuid_new.toString
+                metadataCheckpoint.write(rawMetaProperties.props)
+                uuid_new
+            }
+            uuid_from_properties
+          }
+          case None => {
+            Uuid.randomUuid()
           }
-          dir.getAbsolutePath -> uuid
-        }.toMap
+        }
+        if (s.contains(uuid)) {
+            throw new RuntimeException(s"Found duplicate directory.ids ${uuid.toString}")
+        }
+        s += uuid
+        Seq(dir.getAbsolutePath -> uuid)
       } catch {
         case e: IOException =>
           logDirFailureChannel.maybeAddOfflineLogDir(dir.getAbsolutePath, s"Disk error while loading ID $dir", e)
diff --git a/core/src/main/scala/kafka/server/BrokerMetadataCheckpoint.scala b/core/src/main/scala/kafka/server/BrokerMetadataCheckpoint.scala
index 3d00ebdf3f7c9..21705907347f2 100755
--- a/core/src/main/scala/kafka/server/BrokerMetadataCheckpoint.scala
+++ b/core/src/main/scala/kafka/server/BrokerMetadataCheckpoint.scala
@@ -166,6 +166,7 @@ case class MetaProperties(
   }
 }
 
+// Return only the RawMetaProperties that are the same across all directories.
 object BrokerMetadataCheckpoint extends Logging {
   def getBrokerMetadataAndOfflineDirs(
     logDirs: collection.Seq[String],
@@ -184,6 +185,8 @@ object BrokerMetadataCheckpoint extends Logging {
       try {
         brokerCheckpoint.read() match {
           case Some(properties) =>
+            // XXX Should we check for duplicates here
+            properties.remove(DirectoryIdKey)
             brokerMetadataMap += logDir -> properties
           case None =>
             if (!ignoreMissing) {
diff --git a/core/src/main/scala/kafka/server/KafkaServer.scala b/core/src/main/scala/kafka/server/KafkaServer.scala
index a5a05c977e5d4..350d7b70209a1 100755
--- a/core/src/main/scala/kafka/server/KafkaServer.scala
+++ b/core/src/main/scala/kafka/server/KafkaServer.scala
@@ -63,6 +63,7 @@ import java.io.{File, IOException}
 import java.net.{InetAddress, SocketTimeoutException}
 import java.util.concurrent._
 import java.util.concurrent.atomic.{AtomicBoolean, AtomicInteger}
+import java.util.Properties
 import scala.collection.{Map, Seq}
 import scala.compat.java8.OptionConverters.RichOptionForJava8
 import scala.jdk.CollectionConverters._
@@ -1025,9 +1026,11 @@ class KafkaServer(
    */
   private def checkpointBrokerMetadata(brokerMetadata: ZkMetaProperties) = {
     for (logDir <- config.logDirs if logManager.isLogDirOnline(new File(logDir).getAbsolutePath)) {
+      val props = brokerMetadata.toProperties.clone().asInstanceOf[Properties]
+      props.setProperty("directory.id", logManager.directoryId(logDir).get.toString)
       val checkpoint = brokerMetadataCheckpoints(logDir)
       try {
-        checkpoint.write(brokerMetadata.toProperties)
+        checkpoint.write(props)
       } catch {
         case e: IOException =>
           val dirPath = checkpoint.file.getAbsolutePath
diff --git a/core/src/test/scala/unit/kafka/log/LogManagerTest.scala b/core/src/test/scala/unit/kafka/log/LogManagerTest.scala
index 7e35857c5f731..7a00640b3d1fd 100755
--- a/core/src/test/scala/unit/kafka/log/LogManagerTest.scala
+++ b/core/src/test/scala/unit/kafka/log/LogManagerTest.scala
@@ -1031,9 +1031,34 @@ class LogManagerTest {
 
     assertTrue(logManager.directoryId(dirs(0).getAbsolutePath).isDefined)
     assertEquals(Some(Uuid.fromString("ZwkGXjB0TvSF6mjVh6gO7Q")), logManager.directoryId(dirs(1).getAbsolutePath))
-    assertEquals(None, logManager.directoryId(dirs(2).getAbsolutePath))
+    // We allocate a directoryId even if there isn't a meta.properties.
+    assertTrue(logManager.directoryId(dirs(2).getAbsolutePath).isDefined)
     assertEquals(Some(Uuid.fromString("kQfNPJ2FTHq_6Qlyyv6Jqg")), logManager.directoryId(dirs(3).getAbsolutePath))
     assertTrue(logManager.directoryId(dirs(4).getAbsolutePath).isDefined)
-    assertEquals(4, logManager.directoryIds.size)
+    assertEquals(5, logManager.directoryIds.size)
+  }
+
+  @Test
+  def testLoadDirectoryIdsWithDuplicates(): Unit = {
+    def writeMetaProperties(dir: File, id: Option[String] = None): Unit = {
+      val rawProps = new RawMetaProperties()
+      rawProps.nodeId = 1
+      rawProps.clusterId = "IVT1Seu3QjacxS7oBTKhDQ"
+      id.foreach(v => rawProps.directoryId = v)
+      new BrokerMetadataCheckpoint(new File(dir, KafkaServer.brokerMetaPropsFile)).write(rawProps.props)
+    }
+    val dirs: Seq[File] = Seq.fill(5)(TestUtils.tempDir())
+    writeMetaProperties(dirs(0))
+    writeMetaProperties(dirs(1), Some("ZwkGXjB0TvSF6mjVh6gO7Q"))
+    // no meta.properties on dirs(2)
+    writeMetaProperties(dirs(3), Some("kQfNPJ2FTHq_6Qlyyv6Jqg"))
+    writeMetaProperties(dirs(4), Some("ZwkGXjB0TvSF6mjVh6gO7Q"))
+
+    assertTrue(try {
+       logManager = createLogManager(dirs)
+       false
+    } catch {
+       case e: RuntimeException => true
+    })
   }
 }