diff --git a/paper-server/src/main/java/io/papermc/paper/world/migration/LegacyCraftBukkitWorldMigration.java b/paper-server/src/main/java/io/papermc/paper/world/migration/LegacyCraftBukkitWorldMigration.java
index ba24fda2395f..d186498e9769 100644
--- a/paper-server/src/main/java/io/papermc/paper/world/migration/LegacyCraftBukkitWorldMigration.java
+++ b/paper-server/src/main/java/io/papermc/paper/world/migration/LegacyCraftBukkitWorldMigration.java
@@ -96,8 +96,11 @@ private void run() throws IOException {
             this.migrateLegacyCraftBukkitPaperData(tempStorage, levelDataResult.dataTag());
             tempStorage.saveAndJoin();
         }
-        deleteMigratedSeparateRoot(this.sourceRoot);
-        LOGGER.info("Completed legacy CraftBukkit import for world '{}' ({})", this.context.worldName(), this.context.dimensionKey().identifier());
+
+        final Path oldSourceRoot = this.sourceRoot.resolveSibling(this.sourceRoot.getFileName() + ".old");
+
+        Files.move(this.sourceRoot, oldSourceRoot);
+        LOGGER.info("Completed legacy CraftBukkit import for world '{}' ({}), the old world was moved into '{}'", this.context.worldName(), this.context.dimensionKey().identifier(), oldSourceRoot);
     }
 
     private void migrateSharedSavedData() throws IOException {
@@ -187,18 +190,6 @@ private void copySavedDataIfPresent(
         WorldMigrationSupport.copySavedDataIfPresent(this.sourceDataRoots, this.targetDataRoot, type, true);
     }
 
-    private static void deleteMigratedSeparateRoot(final Path sourceRoot) throws IOException {
-        if (!Files.exists(sourceRoot)) {
-            return;
-        }
-
-        try (final var paths = Files.walk(sourceRoot)) {
-            for (final Path path : paths.sorted(java.util.Comparator.reverseOrder()).toList()) {
-                Files.deleteIfExists(path);
-            }
-        }
-    }
-
     private @Nullable Path findExplicitFile(
         final List<Path> dataRoots,
         final String... relativeCandidates
diff --git a/paper-server/src/main/java/io/papermc/paper/world/migration/WorldMigrationSupport.java b/paper-server/src/main/java/io/papermc/paper/world/migration/WorldMigrationSupport.java
index f961539a3e38..48d8e58cdcf0 100644
--- a/paper-server/src/main/java/io/papermc/paper/world/migration/WorldMigrationSupport.java
+++ b/paper-server/src/main/java/io/papermc/paper/world/migration/WorldMigrationSupport.java
@@ -8,7 +8,9 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.UUID;
 import net.minecraft.core.HolderLookup;
 import net.minecraft.nbt.NbtException;
@@ -88,6 +90,9 @@ static void migrateDimensionDirectories(final Path sourceDimensionRoot, final Pa
             return;
         }
 
+        boolean pathsWithConflicts = false;
+        final HashMap<Path, Path> migrationPaths = new HashMap<>();
+
         for (final String directory : DIMENSION_DIRECTORIES) {
             final Path source = sourceDimensionRoot.resolve(directory);
             if (!Files.exists(source)) {
@@ -95,38 +100,21 @@ static void migrateDimensionDirectories(final Path sourceDimensionRoot, final Pa
             }
 
             final Path target = targetDimensionPath.resolve(directory);
-            LOGGER.info("Migrating world directory from {} to {}", source, target);
-            mergeMove(source, target);
-        }
-    }
-
-    private static void mergeMove(final Path source, final Path target) throws IOException {
-        if (Files.isDirectory(source)) {
-            Files.createDirectories(target);
-            try (final var entries = Files.list(source)) {
-                for (final Path child : entries.toList()) {
-                    mergeMove(child, target.resolve(child.getFileName().toString()));
-                }
+            if (Files.exists(target)) {
+                pathsWithConflicts = true;
+                LOGGER.error("The folder '{}' already exists for dimension {}", directory, targetDimensionPath);
+                continue;
             }
-            tryDeleteIfEmpty(source);
-            return;
+            migrationPaths.put(source, target);
         }
 
-        if (Files.exists(target)) {
-            throw new IOException("Refusing to overwrite existing migrated file " + target + " while moving " + source);
+        if (pathsWithConflicts) {
+            throw new IOException("Refusing to overwrite dimension directories in " + targetDimensionPath + " while migrating from " + sourceDimensionRoot);
         }
 
-        Files.createDirectories(target.getParent());
-        Files.move(source, target);
-    }
-
-    private static void tryDeleteIfEmpty(final Path path) throws IOException {
-        try (final var entries = Files.list(path)) {
-            if (entries.findAny().isPresent()) {
-                return;
-            }
+        for (Map.Entry<Path, Path> entry : migrationPaths.entrySet()) {
+            Files.move(entry.getKey(), entry.getValue());
         }
-        Files.deleteIfExists(path);
     }
 
     record LevelDataResult(@Nullable Dynamic<?> dataTag, boolean fatalError) {}