diff --git a/server/src/main/java/org/elasticsearch/cluster/metadata/Metadata.java b/server/src/main/java/org/elasticsearch/cluster/metadata/Metadata.java
index bfa783ff01160..76319091f4911 100644
--- a/server/src/main/java/org/elasticsearch/cluster/metadata/Metadata.java
+++ b/server/src/main/java/org/elasticsearch/cluster/metadata/Metadata.java
@@ -1230,6 +1230,7 @@ public static Metadata readFrom(StreamInput in) throws IOException {
     }
 
     private static void readBwcCustoms(StreamInput in, Builder builder) throws IOException {
+        final ProjectMetadata.Builder projectBuilder = builder.getProject(ProjectId.DEFAULT);
         final Set<String> clusterScopedNames = in.namedWriteableRegistry().getReaders(ClusterCustom.class).keySet();
         final Set<String> projectScopedNames = in.namedWriteableRegistry().getReaders(ProjectCustom.class).keySet();
         final int count = in.readVInt();
@@ -1245,9 +1246,9 @@ private static void readBwcCustoms(StreamInput in, Builder builder) throws IOExc
                 if (custom instanceof PersistentTasksCustomMetadata persistentTasksCustomMetadata) {
                     final var tuple = persistentTasksCustomMetadata.split();
                     builder.putCustom(tuple.v1().getWriteableName(), tuple.v1());
-                    builder.putProjectCustom(tuple.v2().getWriteableName(), tuple.v2());
+                    projectBuilder.putCustom(tuple.v2().getWriteableName(), tuple.v2());
                 } else {
-                    builder.putProjectCustom(custom.getWriteableName(), custom);
+                    projectBuilder.putCustom(custom.getWriteableName(), custom);
                 }
             } else {
                 throw new IllegalArgumentException("Unknown custom name [" + name + "]");
@@ -1552,7 +1553,8 @@ public Builder putCustom(String type, ClusterCustom custom) {
 
         @Deprecated(forRemoval = true)
         public Builder putCustom(String type, ProjectCustom custom) {
-            return putProjectCustom(type, custom);
+            getSingleProject().putCustom(type, Objects.requireNonNull(custom, type));
+            return this;
         }
 
         public ClusterCustom getCustom(String type) {
@@ -1575,12 +1577,6 @@ public Builder customs(Map<String, ClusterCustom> clusterCustoms) {
             return this;
         }
 
-        @Deprecated(forRemoval = true)
-        public Builder putProjectCustom(String type, ProjectCustom custom) {
-            getSingleProject().putCustom(type, Objects.requireNonNull(custom, type));
-            return this;
-        }
-
         @Deprecated(forRemoval = true)
         public Builder projectCustoms(Map<String, ProjectCustom> projectCustoms) {
             projectCustoms.forEach((key, value) -> Objects.requireNonNull(value, key));
diff --git a/server/src/test/java/org/elasticsearch/cluster/metadata/MetadataPersistentTasksTests.java b/server/src/test/java/org/elasticsearch/cluster/metadata/MetadataPersistentTasksTests.java
index ac3644b6ecc8a..a1780c8a69b5b 100644
--- a/server/src/test/java/org/elasticsearch/cluster/metadata/MetadataPersistentTasksTests.java
+++ b/server/src/test/java/org/elasticsearch/cluster/metadata/MetadataPersistentTasksTests.java
@@ -306,13 +306,16 @@ private Tuple<Metadata, Metadata> randomMetadataAndUpdate() {
                     ClusterPersistentTasksCustomMetadata::new
                 )
             )
-            .putProjectCustom(
-                PersistentTasksCustomMetadata.TYPE,
-                mutatePersistentTasks(
-                    PersistentTasksCustomMetadata.get(before.getProject(Metadata.DEFAULT_PROJECT_ID)),
-                    MetadataPersistentTasksTests::oneProjectPersistentTask,
-                    PersistentTasksCustomMetadata::new
-                )
+            .put(
+                ProjectMetadata.builder(before.getProject(Metadata.DEFAULT_PROJECT_ID))
+                    .putCustom(
+                        PersistentTasksCustomMetadata.TYPE,
+                        mutatePersistentTasks(
+                            PersistentTasksCustomMetadata.get(before.getProject(Metadata.DEFAULT_PROJECT_ID)),
+                            MetadataPersistentTasksTests::oneProjectPersistentTask,
+                            PersistentTasksCustomMetadata::new
+                        )
+                    )
             )
             .build();
         return new Tuple<>(before, after);