diff --git a/connectors/migrations/20250102_clean_zendesk_tickets_articles.ts b/connectors/migrations/20250102_clean_zendesk_tickets_articles.ts
new file mode 100644
index 000000000000..f78cbf2fa624
--- /dev/null
+++ b/connectors/migrations/20250102_clean_zendesk_tickets_articles.ts
@@ -0,0 +1,151 @@
+import { makeScript } from "scripts/helpers";
+import { Op } from "sequelize";
+
+import {
+  getArticleInternalId,
+  getTicketInternalId,
+} from "@connectors/connectors/zendesk/lib/id_conversions";
+import { dataSourceConfigFromConnector } from "@connectors/lib/api/data_source_config";
+import { concurrentExecutor } from "@connectors/lib/async_utils";
+import { deleteDataSourceDocument } from "@connectors/lib/data_sources";
+import { ZendeskArticle, ZendeskTicket } from "@connectors/lib/models/zendesk";
+import type Logger from "@connectors/logger/logger";
+import { ConnectorResource } from "@connectors/resources/connector_resource";
+
+const QUERY_BATCH_SIZE = 256;
+const DOCUMENT_CONCURRENCY = 16;
+
+async function cleanTickets(
+  connector: ConnectorResource,
+  logger: typeof Logger,
+  execute: boolean
+) {
+  let idCursor: number = 0;
+  let tickets: ZendeskTicket[] = [];
+  do {
+    tickets = await ZendeskTicket.findAll({
+      where: {
+        connectorId: connector.id,
+        id: { [Op.gt]: idCursor },
+      },
+      limit: QUERY_BATCH_SIZE,
+      order: [["id", "ASC"]],
+    });
+
+    if (execute) {
+      await concurrentExecutor(
+        tickets,
+        async (ticket) => {
+          return deleteDataSourceDocument(
+            dataSourceConfigFromConnector(connector),
+            // this is the old internal ID
+            getTicketInternalId({
+              connectorId: connector.id,
+              ticketId: ticket.ticketId,
+            })
+          );
+        },
+        { concurrency: DOCUMENT_CONCURRENCY }
+      );
+      logger.info(
+        `LIVE: ${tickets[tickets.length - 1]?.id} >= id > ${idCursor}`
+      );
+    } else {
+      logger.info(
+        `DRY: ${tickets[tickets.length - 1]?.id} >= id > ${idCursor}`
+      );
+    }
+
+    if (tickets.length > 0) {
+      const lastTicket = tickets[tickets.length - 1];
+      if (lastTicket) {
+        idCursor = lastTicket.id;
+      }
+    }
+  } while (tickets.length === QUERY_BATCH_SIZE);
+}
+
+async function cleanArticles(
+  connector: ConnectorResource,
+  logger: typeof Logger,
+  execute: boolean
+) {
+  let idCursor: number = 0;
+  let articles: ZendeskArticle[] = [];
+  do {
+    articles = await ZendeskArticle.findAll({
+      where: {
+        connectorId: connector.id,
+        id: { [Op.gt]: idCursor },
+      },
+      limit: QUERY_BATCH_SIZE,
+      order: [["id", "ASC"]],
+    });
+
+    if (execute) {
+      await concurrentExecutor(
+        articles,
+        async (article) => {
+          return deleteDataSourceDocument(
+            dataSourceConfigFromConnector(connector),
+            // this is the old internal ID
+            getArticleInternalId({
+              connectorId: connector.id,
+              articleId: article.articleId,
+            })
+          );
+        },
+        { concurrency: DOCUMENT_CONCURRENCY }
+      );
+      logger.info(
+        `LIVE: ${articles[articles.length - 1]?.id} >= id > ${idCursor}`
+      );
+    } else {
+      logger.info(
+        `DRY: ${articles[articles.length - 1]?.id} >= id > ${idCursor}`
+      );
+    }
+
+    if (articles.length > 0) {
+      const lastTicket = articles[articles.length - 1];
+      if (lastTicket) {
+        idCursor = lastTicket.id;
+      }
+    }
+  } while (articles.length === QUERY_BATCH_SIZE);
+}
+
+makeScript(
+  { resourceType: { type: "string", choices: ["tickets", "articles"] } },
+  async ({ execute, resourceType }, logger) => {
+    const connectors = await ConnectorResource.listByType("zendesk", {});
+
+    switch (resourceType) {
+      case "tickets": {
+        for (const connector of connectors) {
+          logger.info({ connectorId: connector.id }, `MIGRATING`);
+          await cleanTickets(
+            connector,
+            logger.child({ connectorId: connector.id }),
+            execute
+          );
+        }
+        break;
+      }
+      case "articles": {
+        for (const connector of connectors) {
+          logger.info({ connectorId: connector.id }, `MIGRATING`);
+          await cleanArticles(
+            connector,
+            logger.child({ connectorId: connector.id }),
+            execute
+          );
+        }
+        break;
+      }
+      default: {
+        throw new Error(`Invalid resource type: ${resourceType}`);
+      }
+    }
+  }
+);
diff --git a/connectors/src/connectors/zendesk/lib/id_conversions.ts b/connectors/src/connectors/zendesk/lib/id_conversions.ts
index 611f321794b7..ce4b5b9feac8 100644
--- a/connectors/src/connectors/zendesk/lib/id_conversions.ts
+++ b/connectors/src/connectors/zendesk/lib/id_conversions.ts
@@ -47,6 +47,18 @@ export function getArticleInternalId({
   return `zendesk-article-${connectorId}-${articleId}`;
 }
 
+export function getArticleNewInternalId({
+  connectorId,
+  brandId,
+  articleId,
+}: {
+  connectorId: ModelId;
+  brandId: number;
+  articleId: number;
+}): string {
+  return `zendesk-article-${connectorId}-${brandId}-${articleId}`;
+}
+
 export function getTicketsInternalId({
   connectorId,
   brandId,
@@ -67,6 +79,18 @@ export function getTicketInternalId({
   return `zendesk-ticket-${connectorId}-${ticketId}`;
 }
 
+export function getTicketNewInternalId({
+  connectorId,
+  brandId,
+  ticketId,
+}: {
+  connectorId: ModelId;
+  brandId: number;
+  ticketId: number;
+}): string {
+  return `zendesk-ticket-${connectorId}-${brandId}-${ticketId}`;
+}
+
 /**
  * Conversion from an internalId to an id.
  */
diff --git a/connectors/src/connectors/zendesk/lib/sync_article.ts b/connectors/src/connectors/zendesk/lib/sync_article.ts
index ed3d7ddabbf6..bd86eadd9593 100644
--- a/connectors/src/connectors/zendesk/lib/sync_article.ts
+++ b/connectors/src/connectors/zendesk/lib/sync_article.ts
@@ -6,7 +6,10 @@ import type {
   ZendeskFetchedSection,
   ZendeskFetchedUser,
 } from "@connectors/@types/node-zendesk";
-import { getArticleInternalId } from "@connectors/connectors/zendesk/lib/id_conversions";
+import {
+  getArticleInternalId,
+  getArticleNewInternalId,
+} from "@connectors/connectors/zendesk/lib/id_conversions";
 import {
   deleteDataSourceDocument,
   renderDocumentTitleAndContent,
@@ -146,15 +149,27 @@ export async function syncArticle({
       updatedAt,
     });
 
-    const documentId = getArticleInternalId({
+    const oldDocumentId = getArticleInternalId({
       connectorId,
       articleId: article.id,
     });
 
+    // TODO(2025-01-02 aubin): stop deleting old documents once the migration of internal IDs is done.
+    await deleteDataSourceDocument(dataSourceConfig, oldDocumentId, {
+      ...loggerArgs,
+      articleId: article.id,
+    });
+
     const parents = articleInDb.getParentInternalIds(connectorId);
+    const newDocumentId = getArticleNewInternalId({
+      connectorId,
+      brandId: category.brandId,
+      articleId: article.id,
+    });
+
     await upsertDataSourceDocument({
       dataSourceConfig,
-      documentId,
+      documentId: newDocumentId,
       documentContent,
       documentUrl: article.html_url,
       timestampMs: updatedAt.getTime(),
@@ -163,7 +178,7 @@ export async function syncArticle({
         `createdAt:${createdAt.getTime()}`,
         `updatedAt:${updatedAt.getTime()}`,
       ],
-      parents,
+      parents: [newDocumentId, ...parents.slice(1)],
       parentId: parents[1],
       loggerArgs: { ...loggerArgs, articleId: article.id },
       upsertContext: { sync_type: "batch" },
@@ -171,6 +186,7 @@ export async function syncArticle({
       mimeType: "application/vnd.dust.zendesk.article",
       async: true,
     });
+
     await articleInDb.update({ lastUpsertedTs: new Date(currentSyncDateMs) });
   } else {
     logger.warn(
diff --git a/connectors/src/connectors/zendesk/lib/sync_ticket.ts b/connectors/src/connectors/zendesk/lib/sync_ticket.ts
index b626b53fd5c6..d51a5e154a17 100644
--- a/connectors/src/connectors/zendesk/lib/sync_ticket.ts
+++ b/connectors/src/connectors/zendesk/lib/sync_ticket.ts
@@ -6,7 +6,10 @@ import type {
   ZendeskFetchedTicketComment,
   ZendeskFetchedUser,
 } from "@connectors/@types/node-zendesk";
-import { getTicketInternalId } from "@connectors/connectors/zendesk/lib/id_conversions";
+import {
+  getTicketInternalId,
+  getTicketNewInternalId,
+} from "@connectors/connectors/zendesk/lib/id_conversions";
 import {
   deleteDataSourceDocument,
   renderDocumentTitleAndContent,
@@ -204,15 +207,26 @@ ${comments
       updatedAt: updatedAtDate,
     });
 
-    const documentId = getTicketInternalId({
+    const oldDocumentId = getTicketInternalId({
       connectorId,
       ticketId: ticket.id,
     });
+    // TODO(2025-01-02 aubin): stop deleting old documents once the migration of internal IDs is done.
+    await deleteDataSourceDocument(dataSourceConfig, oldDocumentId, {
+      ...loggerArgs,
+      ticketId: ticket.id,
+    });
 
     const parents = ticketInDb.getParentInternalIds(connectorId);
+    const newDocumentId = getTicketNewInternalId({
+      connectorId,
+      brandId,
+      ticketId: ticket.id,
+    });
+
     await upsertDataSourceDocument({
       dataSourceConfig,
-      documentId,
+      documentId: newDocumentId,
       documentContent,
       documentUrl: ticket.url,
       timestampMs: updatedAtDate.getTime(),
@@ -222,7 +236,7 @@ ${comments
         `updatedAt:${updatedAtDate.getTime()}`,
         `createdAt:${createdAtDate.getTime()}`,
       ],
-      parents,
+      parents: [newDocumentId, ...parents.slice(1)],
       parentId: parents[1],
       loggerArgs: { ...loggerArgs, ticketId: ticket.id },
       upsertContext: { sync_type: "batch" },
@@ -230,6 +244,7 @@ ${comments
       mimeType: "application/vnd.dust.zendesk.ticket",
       async: true,
     });
+
     await ticketInDb.update({ lastUpsertedTs: new Date(currentSyncDateMs) });
   } else {
     logger.warn(