diff --git a/backend/src/db/migrations/20250507185010_pit-projects-commits-initialization.ts b/backend/src/db/migrations/20250507185010_pit-projects-commits-initialization.ts
index 459727035..3fa57bb98 100644
--- a/backend/src/db/migrations/20250507185010_pit-projects-commits-initialization.ts
+++ b/backend/src/db/migrations/20250507185010_pit-projects-commits-initialization.ts
@@ -1,23 +1,231 @@
 import { Knex } from "knex";
 
 import { inMemoryKeyStore } from "@app/keystore/memory";
+import { chunkArray } from "@app/lib/fn";
+import { selectAllTableCols } from "@app/lib/knex";
+import { logger } from "@app/lib/logger";
 
-import { ProjectType, TableName } from "../schemas";
+import {
+  ProjectType,
+  TableName,
+  TFolderCheckpoints,
+  TFolderCommits,
+  TFolderTreeCheckpoints,
+  TSecretFolders
+} from "../schemas";
 import { getMigrationEnvConfig } from "./utils/env-config";
 import { getMigrationPITServices } from "./utils/services";
 
+const sortFoldersByHierarchy = (folders: TSecretFolders[]) => {
+  // Create a map for quick lookup of children by parent ID
+  const childrenMap = new Map<string, TSecretFolders[]>();
+
+  // Set of all folder IDs
+  const allFolderIds = new Set<string>();
+
+  // Build the set of all folder IDs
+  folders.forEach((folder) => {
+    if (folder.id) {
+      allFolderIds.add(folder.id);
+    }
+  });
+
+  // Group folders by their parentId
+  folders.forEach((folder) => {
+    if (folder.parentId) {
+      const children = childrenMap.get(folder.parentId) || [];
+      children.push(folder);
+      childrenMap.set(folder.parentId, children);
+    }
+  });
+
+  // Find root folders - those with no parentId or with a parentId that doesn't exist
+  const rootFolders = folders.filter((folder) => !folder.parentId || !allFolderIds.has(folder.parentId));
+
+  // Process each level of the hierarchy
+  const result = [];
+  let currentLevel = rootFolders;
+
+  while (currentLevel.length > 0) {
+    result.push(...currentLevel);
+
+    const nextLevel = [];
+    for (const folder of currentLevel) {
+      if (folder.id) {
+        const children = childrenMap.get(folder.id) || [];
+        nextLevel.push(...children);
+      }
+    }
+
+    currentLevel = nextLevel;
+  }
+
+  return result.reverse();
+};
+
 export async function up(knex: Knex): Promise<void> {
+  logger.info("Initializing folder commits");
   const hasFolderCommitTable = await knex.schema.hasTable(TableName.FolderCommit);
   if (hasFolderCommitTable) {
     const keyStore = inMemoryKeyStore();
     const envConfig = getMigrationEnvConfig();
     const { folderCommitService } = await getMigrationPITServices({ db: knex, keyStore, envConfig });
-    const projects = await knex(TableName.Project).where({ version: 3, type: ProjectType.SecretManager }).select("id");
-    for (const project of projects) {
+
+    // Get Projects to Initialize
+    const projects = await knex(TableName.Project)
+      .where(`${TableName.Project}.version`, 3)
+      .where(`${TableName.Project}.type`, ProjectType.SecretManager)
+      .select(selectAllTableCols(TableName.Project));
+    logger.info(`Found ${projects.length} projects to initialize`);
+
+    // Process Projects in batches of 100
+    const batches = chunkArray(projects, 100);
+    let i = 0;
+    for (const batch of batches) {
+      i += 1;
+      logger.info(`Processing project batch ${i} of ${batches.length}`);
+      const foldersCommitsList = [];
+
+      const rootFoldersMap: Record<string, string> = {};
+
+      // Get All Folders for the Project
       // eslint-disable-next-line no-await-in-loop
-      await folderCommitService.initializeProject(project.id, knex);
+      const folders = await knex(TableName.SecretFolder)
+        .join(TableName.Environment, `${TableName.SecretFolder}.envId`, `${TableName.Environment}.id`)
+        .whereIn(
+          `${TableName.Environment}.projectId`,
+          batch.map((project) => project.id)
+        )
+        .select(selectAllTableCols(TableName.SecretFolder));
+      logger.info(`Found ${folders.length} folders to initialize in project batch ${i} of ${batches.length}`);
+
+      // Sort Folders by Hierarchy (parents before nested folders)
+      const sortedFolders = sortFoldersByHierarchy(folders);
+
+      // Get folder commit changes
+      for (const folder of sortedFolders) {
+        // eslint-disable-next-line no-await-in-loop
+        const folderCommit = await folderCommitService.getFolderInitialChanges(folder.id, folder.envId, knex);
+        if (folderCommit.commit && folderCommit.changes) {
+          foldersCommitsList.push(folderCommit);
+          if (!folder.parentId) {
+            rootFoldersMap[folder.id] = folder.envId;
+          }
+        }
+      }
+      logger.info(`Retrieved folder changes for project batch ${i} of ${batches.length}`);
+
+      // Insert New Commits in batches of 9000
+      const newCommits = foldersCommitsList.map((folderCommit) => folderCommit.commit);
+      const commitBatches = chunkArray(newCommits, 9000);
+
+      let j = 0;
+      for (const commitBatch of commitBatches) {
+        j += 1;
+        logger.info(`Inserting folder commits - batch ${j} of ${commitBatches.length}`);
+        // Create folder commit
+        // eslint-disable-next-line no-await-in-loop
+        const newCommitsInserted = (await knex
+          .batchInsert(TableName.FolderCommit, commitBatch)
+          .returning("*")) as TFolderCommits[];
+
+        logger.info(`Finished inserting folder commits - batch ${j} of ${commitBatches.length}`);
+
+        const newCommitsMap: Record<string, string> = {};
+        const newCommitsMapInverted: Record<string, string> = {};
+        const newCheckpointsMap: Record<string, string> = {};
+        newCommitsInserted.forEach((commit) => {
+          newCommitsMap[commit.folderId] = commit.id;
+          newCommitsMapInverted[commit.id] = commit.folderId;
+        });
+
+        // Create folder checkpoints
+        // eslint-disable-next-line no-await-in-loop
+        const newCheckpoints = (await knex
+          .batchInsert(
+            TableName.FolderCheckpoint,
+            Object.values(newCommitsMap).map((commitId) => ({
+              folderCommitId: commitId
+            }))
+          )
+          .returning("*")) as TFolderCheckpoints[];
+
+        logger.info(`Finished inserting folder checkpoints - batch ${j} of ${commitBatches.length}`);
+
+        newCheckpoints.forEach((checkpoint) => {
+          newCheckpointsMap[newCommitsMapInverted[checkpoint.folderCommitId]] = checkpoint.id;
+        });
+
+        // Create folder commit changes
+        // eslint-disable-next-line no-await-in-loop
+        await knex.batchInsert(
+          TableName.FolderCommitChanges,
+          foldersCommitsList
+            .map((folderCommit) => folderCommit.changes)
+            .flat()
+            .map((change) => ({
+              folderCommitId: newCommitsMap[change.folderId],
+              changeType: change.changeType,
+              secretVersionId: change.secretVersionId,
+              folderVersionId: change.folderVersionId,
+              isUpdate: false
+            }))
+        );
+
+        logger.info(`Finished inserting folder commit changes - batch ${j} of ${commitBatches.length}`);
+
+        // Create folder checkpoint resources
+        // eslint-disable-next-line no-await-in-loop
+        await knex.batchInsert(
+          TableName.FolderCheckpointResources,
+          foldersCommitsList
+            .map((folderCommit) => folderCommit.changes)
+            .flat()
+            .map((change) => ({
+              folderCheckpointId: newCheckpointsMap[change.folderId],
+              folderVersionId: change.folderVersionId,
+              secretVersionId: change.secretVersionId
+            }))
+        );
+
+        logger.info(`Finished inserting folder checkpoint resources - batch ${j} of ${commitBatches.length}`);
+
+        // Create Folder Tree Checkpoint
+        // eslint-disable-next-line no-await-in-loop
+        const newTreeCheckpoints = (await knex
+          .batchInsert(
+            TableName.FolderTreeCheckpoint,
+            Object.keys(rootFoldersMap).map((folderId) => ({
+              folderCommitId: newCommitsMap[folderId]
+            }))
+          )
+          .returning("*")) as TFolderTreeCheckpoints[];
+
+        logger.info(`Finished inserting folder tree checkpoints - batch ${j} of ${commitBatches.length}`);
+
+        const newTreeCheckpointsMap: Record<string, string> = {};
+        newTreeCheckpoints.forEach((checkpoint) => {
+          newTreeCheckpointsMap[rootFoldersMap[newCommitsMapInverted[checkpoint.folderCommitId]]] = checkpoint.id;
+        });
+
+        // Create Folder Tree Checkpoint Resources
+        // eslint-disable-next-line no-await-in-loop
+        await knex
+          .batchInsert(
+            TableName.FolderTreeCheckpointResources,
+            newCommitsInserted.map((folderCommit) => ({
+              folderTreeCheckpointId: newTreeCheckpointsMap[folderCommit.envId],
+              folderId: folderCommit.folderId,
+              folderCommitId: folderCommit.id
+            }))
+          )
+          .returning("*");
+
+        logger.info(`Finished inserting folder tree checkpoint resources - batch ${j} of ${commitBatches.length}`);
+      }
     }
   }
+  logger.info("Folder commits initialized");
 }
 
 export async function down(knex: Knex): Promise<void> {
diff --git a/backend/src/services/folder-commit/folder-commit-service.ts b/backend/src/services/folder-commit/folder-commit-service.ts
index 8fe89e8c2..aac3804aa 100644
--- a/backend/src/services/folder-commit/folder-commit-service.ts
+++ b/backend/src/services/folder-commit/folder-commit-service.ts
@@ -240,12 +240,19 @@ export const folderCommitServiceFactory = ({
     if (subFolders.length > 0) {
       const subFolderIds = subFolders.map((folder) => folder.id);
       const folderVersions = await folderVersionDAL.findLatestFolderVersions(subFolderIds, tx);
-      resources.push(...Object.values(folderVersions).map((folderVersion) => ({ folderVersionId: folderVersion.id })));
+      resources.push(
+        ...Object.values(folderVersions).map((folderVersion) => ({
+          folderVersionId: folderVersion.id,
+          secretVersionId: undefined
+        }))
+      );
     }
 
     const secretVersions = await secretVersionV2BridgeDAL.findLatestVersionByFolderId(folderId, tx);
     if (secretVersions.length > 0) {
-      resources.push(...secretVersions.map((secretVersion) => ({ secretVersionId: secretVersion.id })));
+      resources.push(
+        ...secretVersions.map((secretVersion) => ({ secretVersionId: secretVersion.id, folderVersionId: undefined }))
+      );
     }
 
     return resources;
@@ -1574,27 +1581,29 @@ export const folderCommitServiceFactory = ({
   /**
    * Initialize a folder with its current state
    */
-  const initializeFolder = async (folderId: string, tx?: Knex) => {
+  const getFolderInitialChanges = async (folderId: string, envId: string, tx?: Knex) => {
     const folderResources = await getFolderResources(folderId, tx);
     const changes = folderResources.map((resource) => ({ type: ChangeType.ADD, ...resource }));
 
     if (changes.length > 0) {
-      const newCommit = await createCommit(
-        {
-          actor: {
-            type: ActorType.PLATFORM
-          },
+      return {
+        commit: {
+          actorMetadata: {},
+          actorType: ActorType.PLATFORM,
           message: "Initialized folder",
           folderId,
-          changes,
-          omitIgnoreFilter: true
+          envId
         },
-        tx
-      );
-      if (newCommit) {
-        await createFolderCheckpoint({ folderId, folderCommitId: newCommit.id, force: true, tx });
-      }
+        changes: changes.map((change) => ({
+          folderId,
+          changeType: change.type,
+          secretVersionId: change.secretVersionId,
+          folderVersionId: change.folderVersionId,
+          isUpdate: false
+        }))
+      };
     }
+    return {};
   };
 
   /**
@@ -1697,33 +1706,6 @@ export const folderCommitServiceFactory = ({
     );
   };
 
-  /**
-   * Initialize a project with its current state
-   */
-  const initializeProject = async (projectId: string, tx?: Knex) => {
-    const project = await projectDAL.findById(projectId, tx);
-    if (!project) {
-      throw new NotFoundError({ message: `Project with ID ${projectId} not found` });
-    }
-
-    const folders = await folderDAL.findByProjectId(projectId, tx);
-    const sortedFolders = sortFoldersByHierarchy(folders);
-
-    const batchSize = 5;
-    const chunks = chunkArray(sortedFolders, batchSize);
-
-    for (const chunk of chunks) {
-      await Promise.all(chunk.map((folder) => initializeFolder(folder.id, tx)));
-    }
-
-    const envIds = [...new Set(folders.map((folder) => folder.envId))];
-    await Promise.all(
-      envIds.map(async (envId) => {
-        await createFolderTreeCheckpoint(envId, undefined, tx);
-      })
-    );
-  };
-
   const addNestedFolderChanges = async ({
     changes,
     beforeCommit,
@@ -2173,8 +2155,7 @@ export const folderCommitServiceFactory = ({
     getCommitChanges,
     getCheckpointsByFolderId,
     getLatestCheckpoint,
-    initializeFolder,
-    initializeProject,
+    getFolderInitialChanges,
     createFolderCheckpoint,
     compareFolderStates,
     applyFolderStateDifferences,