diff --git a/server/queues/tasks/ExportDocumentTreeTask.ts b/server/queues/tasks/ExportDocumentTreeTask.ts
new file mode 100644
index 000000000..edaa0ed90
--- /dev/null
+++ b/server/queues/tasks/ExportDocumentTreeTask.ts
@@ -0,0 +1,195 @@
+import path from "path";
+import JSZip from "jszip";
+import { FileOperationFormat } from "@shared/types";
+import Logger from "@server/logging/Logger";
+import { Collection } from "@server/models";
+import Attachment from "@server/models/Attachment";
+import Document from "@server/models/Document";
+import DocumentHelper from "@server/models/helpers/DocumentHelper";
+import ZipHelper from "@server/utils/ZipHelper";
+import { serializeFilename } from "@server/utils/fs";
+import parseAttachmentIds from "@server/utils/parseAttachmentIds";
+import { getFileByKey } from "@server/utils/s3";
+import { NavigationNode } from "~/types";
+import ExportTask from "./ExportTask";
+
+export default abstract class ExportDocumentTreeTask extends ExportTask {
+  /**
+   * Exports the document tree to the given zip instance.
+   *
+   * @param zip The JSZip instance to add files to
+   * @param documentId The document ID to export
+   * @param pathInZip The path in the zip to add the document to
+   * @param format The format to export in
+   */
+  protected async addDocumentToArchive({
+    zip,
+    pathInZip,
+    documentId,
+    format = FileOperationFormat.MarkdownZip,
+    pathMap,
+  }: {
+    zip: JSZip;
+    pathInZip: string;
+    documentId: string;
+    format: FileOperationFormat;
+    pathMap: Map<string, string>;
+  }) {
+    const document = await Document.findByPk(documentId);
+    if (!document) {
+      return;
+    }
+
+    let text =
+      format === FileOperationFormat.HTMLZip
+        ? await DocumentHelper.toHTML(document, { centered: true })
+        : await DocumentHelper.toMarkdown(document);
+    const attachments = await Attachment.findAll({
+      where: {
+        teamId: document.teamId,
+        id: parseAttachmentIds(document.text),
+      },
+    });
+
+    // Add any referenced attachments to the zip file and replace the
+    // reference in the document with the path to the attachment in the zip
+    await Promise.all(
+      attachments.map(async (attachment) => {
+        try {
+          const img = await getFileByKey(attachment.key);
+          const dir = path.dirname(pathInZip);
+          if (img) {
+            zip.file(path.join(dir, attachment.key), img as Blob, {
+              createFolders: true,
+            });
+          }
+        } catch (err) {
+          Logger.error(
+            `Failed to add attachment to archive: ${attachment.key}`,
+            err
+          );
+        }
+
+        text = text.replace(attachment.redirectUrl, encodeURI(attachment.key));
+      })
+    );
+
+    // Replace any internal links with relative paths to the document in the zip
+    const internalLinks = [
+      ...text.matchAll(/\/doc\/(?:[0-9a-zA-Z-_~]*-)?([a-zA-Z0-9]{10,15})/g),
+    ];
+    internalLinks.forEach((match) => {
+      const matchedLink = match[0];
+      const matchedDocPath = pathMap.get(matchedLink);
+
+      if (matchedDocPath) {
+        const relativePath = path.relative(pathInZip, matchedDocPath);
+        if (relativePath.startsWith(".")) {
+          text = text.replace(
+            matchedLink,
+            encodeURI(relativePath.substring(1))
+          );
+        }
+      }
+    });
+
+    // Finally, add the document to the zip file
+    zip.file(pathInZip, text, {
+      date: document.updatedAt,
+      createFolders: true,
+      comment: JSON.stringify({
+        createdAt: document.createdAt,
+        updatedAt: document.updatedAt,
+      }),
+    });
+  }
+
+  /**
+   * Exports the documents and attachments in the given collections to a zip file
+   * and returns the path to the zip file in tmp.
+   *
+   * @param zip The JSZip instance to add files to
+   * @param collections The collections to export
+   * @param format The format to export in
+   *
+   * @returns The path to the zip file in tmp.
+   */
+  protected async addCollectionsToArchive(
+    zip: JSZip,
+    collections: Collection[],
+    format: FileOperationFormat
+  ) {
+    const pathMap = this.createPathMap(collections, format);
+
+    for (const path of pathMap) {
+      const documentId = path[0].replace("/doc/", "");
+      const pathInZip = path[1];
+
+      await this.addDocumentToArchive({
+        zip,
+        pathInZip,
+        documentId,
+        format,
+        pathMap,
+      });
+    }
+
+    return ZipHelper.toTmpFile(zip);
+  }
+
+  /**
+   * Generates a map of document urls to their path in the zip file.
+   *
+   * @param collections
+   */
+  private createPathMap(
+    collections: Collection[],
+    format: FileOperationFormat
+  ) {
+    const map = new Map<string, string>();
+
+    for (const collection of collections) {
+      if (collection.documentStructure) {
+        this.addDocumentTreeToPathMap(
+          map,
+          collection.documentStructure,
+          serializeFilename(collection.name),
+          format
+        );
+      }
+    }
+
+    return map;
+  }
+
+  private addDocumentTreeToPathMap(
+    map: Map<string, string>,
+    nodes: NavigationNode[],
+    root: string,
+    format: FileOperationFormat
+  ) {
+    for (const node of nodes) {
+      const title = serializeFilename(node.title) || "Untitled";
+      const extension = format === FileOperationFormat.HTMLZip ? "html" : "md";
+
+      // Ensure the document is given a unique path in zip, even if it has
+      // the same title as another document in the same collection.
+      let i = 0;
+      let filePath = path.join(root, `${title}.${extension}`);
+      while (Array.from(map.values()).includes(filePath)) {
+        filePath = path.join(root, `${title} (${++i}).${extension}`);
+      }
+
+      map.set(node.url, filePath);
+
+      if (node.children?.length) {
+        this.addDocumentTreeToPathMap(
+          map,
+          node.children,
+          path.join(root, title),
+          format
+        );
+      }
+    }
+  }
+}
diff --git a/server/queues/tasks/ExportHTMLZipTask.ts b/server/queues/tasks/ExportHTMLZipTask.ts
index aabdfafa6..fc6a84ef9 100644
--- a/server/queues/tasks/ExportHTMLZipTask.ts
+++ b/server/queues/tasks/ExportHTMLZipTask.ts
@@ -1,10 +1,16 @@
+import JSZip from "jszip";
 import { FileOperationFormat } from "@shared/types";
 import { Collection } from "@server/models";
-import { archiveCollections } from "@server/utils/zip";
-import ExportTask from "./ExportTask";
+import ExportDocumentTreeTask from "./ExportDocumentTreeTask";
 
-export default class ExportHTMLZipTask extends ExportTask {
+export default class ExportHTMLZipTask extends ExportDocumentTreeTask {
   public async export(collections: Collection[]) {
-    return await archiveCollections(collections, FileOperationFormat.HTMLZip);
+    const zip = new JSZip();
+
+    return await this.addCollectionsToArchive(
+      zip,
+      collections,
+      FileOperationFormat.HTMLZip
+    );
   }
 }
diff --git a/server/queues/tasks/ExportMarkdownZipTask.ts b/server/queues/tasks/ExportMarkdownZipTask.ts
index a84a93cb6..6ea69eefe 100644
--- a/server/queues/tasks/ExportMarkdownZipTask.ts
+++ b/server/queues/tasks/ExportMarkdownZipTask.ts
@@ -1,11 +1,14 @@
+import JSZip from "jszip";
 import { FileOperationFormat } from "@shared/types";
 import { Collection } from "@server/models";
-import { archiveCollections } from "@server/utils/zip";
-import ExportTask from "./ExportTask";
+import ExportDocumentTreeTask from "./ExportDocumentTreeTask";
 
-export default class ExportMarkdownZipTask extends ExportTask {
+export default class ExportMarkdownZipTask extends ExportDocumentTreeTask {
   public async export(collections: Collection[]) {
-    return await archiveCollections(
+    const zip = new JSZip();
+
+    return await this.addCollectionsToArchive(
+      zip,
       collections,
       FileOperationFormat.MarkdownZip
     );
diff --git a/server/queues/tasks/ImportMarkdownZipTask.ts b/server/queues/tasks/ImportMarkdownZipTask.ts
index 4053619fd..966f8240e 100644
--- a/server/queues/tasks/ImportMarkdownZipTask.ts
+++ b/server/queues/tasks/ImportMarkdownZipTask.ts
@@ -5,7 +5,7 @@ import { v4 as uuidv4 } from "uuid";
 import documentImporter from "@server/commands/documentImporter";
 import Logger from "@server/logging/Logger";
 import { FileOperation, User } from "@server/models";
-import { zipAsFileTree, FileTreeNode } from "@server/utils/zip";
+import ZipHelper, { FileTreeNode } from "@server/utils/ZipHelper";
 import ImportTask, { StructuredImportData } from "./ImportTask";
 
 export default class ImportMarkdownZipTask extends ImportTask {
@@ -14,7 +14,7 @@ export default class ImportMarkdownZipTask extends ImportTask {
     fileOperation: FileOperation
   ): Promise<StructuredImportData> {
     const zip = await JSZip.loadAsync(buffer);
-    const tree = zipAsFileTree(zip);
+    const tree = ZipHelper.toFileTree(zip);
 
     return this.parseFileTree({ fileOperation, zip, tree });
   }
diff --git a/server/queues/tasks/ImportNotionTask.ts b/server/queues/tasks/ImportNotionTask.ts
index bcbaa8c25..7b67523e2 100644
--- a/server/queues/tasks/ImportNotionTask.ts
+++ b/server/queues/tasks/ImportNotionTask.ts
@@ -6,7 +6,7 @@ import { v4 as uuidv4 } from "uuid";
 import documentImporter from "@server/commands/documentImporter";
 import Logger from "@server/logging/Logger";
 import { FileOperation, User } from "@server/models";
-import { zipAsFileTree, FileTreeNode } from "@server/utils/zip";
+import ZipHelper, { FileTreeNode } from "@server/utils/ZipHelper";
 import ImportTask, { StructuredImportData } from "./ImportTask";
 
 export default class ImportNotionTask extends ImportTask {
@@ -15,7 +15,7 @@ export default class ImportNotionTask extends ImportTask {
     fileOperation: FileOperation
   ): Promise<StructuredImportData> {
     const zip = await JSZip.loadAsync(buffer);
-    const tree = zipAsFileTree(zip);
+    const tree = ZipHelper.toFileTree(zip);
     return this.parseFileTree({ fileOperation, zip, tree });
   }
 
diff --git a/server/utils/ZipHelper.ts b/server/utils/ZipHelper.ts
new file mode 100644
index 000000000..bc15f267d
--- /dev/null
+++ b/server/utils/ZipHelper.ts
@@ -0,0 +1,115 @@
+import fs from "fs";
+import path from "path";
+import JSZip from "jszip";
+import { find } from "lodash";
+import tmp from "tmp";
+import { ValidationError } from "@server/errors";
+import { trace } from "@server/logging/tracing";
+import { deserializeFilename } from "./fs";
+
+export type FileTreeNode = {
+  /** The title, extracted from the file name */
+  title: string;
+  /** The file name including extension */
+  name: string;
+  /** Full path to the file within the zip file */
+  path: string;
+  /** Any nested children */
+  children: FileTreeNode[];
+};
+
+@trace()
+export default class ZipHelper {
+  /**
+   * Converts the flat structure returned by JSZIP into a nested file structure
+   * for easier processing.
+   *
+   * @param zip The JSZip instance
+   * @param maxFiles The maximum number of files to unzip (Prevent zip bombs)
+   */
+  public static toFileTree(
+    zip: JSZip,
+    /** The maximum number of files to unzip */
+    maxFiles = 10000
+  ) {
+    let fileCount = 0;
+    const paths = Object.keys(zip.files).map((filePath) => {
+      if (++fileCount > maxFiles) {
+        throw ValidationError("Too many files in zip");
+      }
+
+      return `/${filePath}`;
+    });
+    const tree: FileTreeNode[] = [];
+
+    paths.forEach(function (filePath) {
+      if (filePath.startsWith("/__MACOSX")) {
+        return;
+      }
+
+      const pathParts = filePath.split("/");
+
+      // Remove first blank element from the parts array.
+      pathParts.shift();
+
+      let currentLevel = tree; // initialize currentLevel to root
+
+      pathParts.forEach(function (name) {
+        // check to see if the path already exists.
+        const existingPath = find(currentLevel, {
+          name,
+        });
+
+        if (existingPath) {
+          // The path to this item was already in the tree, so don't add again.
+          // Set the current level to this path's children
+          currentLevel = existingPath.children;
+        } else if (name.endsWith(".DS_Store") || !name) {
+          return;
+        } else {
+          const newPart = {
+            name,
+            path: filePath.replace(/^\//, ""),
+            title: deserializeFilename(path.parse(path.basename(name)).name),
+            children: [],
+          };
+
+          currentLevel.push(newPart);
+          currentLevel = newPart.children;
+        }
+      });
+    });
+
+    return tree;
+  }
+
+  /**
+   * Write a zip file to a temporary disk location
+   *
+   * @param zip JSZip object
+   * @returns pathname of the temporary file where the zip was written to disk
+   */
+  public static async toTmpFile(zip: JSZip): Promise<string> {
+    return new Promise((resolve, reject) => {
+      tmp.file(
+        {
+          prefix: "export-",
+          postfix: ".zip",
+        },
+        (err, path) => {
+          if (err) {
+            return reject(err);
+          }
+          zip
+            .generateNodeStream({
+              type: "nodebuffer",
+              streamFiles: true,
+            })
+            .pipe(fs.createWriteStream(path))
+            .on("finish", () => resolve(path))
+            .on("error", reject);
+        }
+      );
+    });
+  }
+}
diff --git a/server/utils/zip.ts b/server/utils/zip.ts
deleted file mode 100644
index 8882b216c..000000000
--- a/server/utils/zip.ts
+++ /dev/null
@@ -1,266 +0,0 @@
-import fs from "fs";
-import path from "path";
-import JSZip, { JSZipObject } from "jszip";
-import { find } from "lodash";
-import tmp from "tmp";
-import { FileOperationFormat } from "@shared/types";
-import { ValidationError } from "@server/errors";
-import Logger from "@server/logging/Logger";
-import Attachment from "@server/models/Attachment";
-import Collection from "@server/models/Collection";
-import Document from "@server/models/Document";
-import DocumentHelper from "@server/models/helpers/DocumentHelper";
-import { NavigationNode } from "~/types";
-import { deserializeFilename, serializeFilename } from "./fs";
-import parseAttachmentIds from "./parseAttachmentIds";
-import { getFileByKey } from "./s3";
-
-type ItemType = "collection" | "document" | "attachment";
-
-export type Item = {
-  path: string;
-  dir: string;
-  name: string;
-  depth: number;
-  metadata: Record<string, any>;
-  type: ItemType;
-  item: JSZipObject;
-};
-
-export type FileTreeNode = {
-  /** The title, extracted from the file name */
-  title: string;
-  /** The file name including extension */
-  name: string;
-  /** The full path to within the zip file */
-  path: string;
-  /** The nested children */
-  children: FileTreeNode[];
-};
-
-async function addDocumentTreeToArchive(
-  zip: JSZip,
-  documents: NavigationNode[],
-  format = FileOperationFormat.MarkdownZip
-) {
-  for (const doc of documents) {
-    const document = await Document.findByPk(doc.id);
-
-    if (!document) {
-      continue;
-    }
-
-    let text =
-      format === FileOperationFormat.HTMLZip
-        ? await DocumentHelper.toHTML(document, { centered: true })
-        : await DocumentHelper.toMarkdown(document);
-    const attachments = await Attachment.findAll({
-      where: {
-        teamId: document.teamId,
-        id: parseAttachmentIds(document.text),
-      },
-    });
-
-    for (const attachment of attachments) {
-      await addImageToArchive(zip, attachment.key);
-      text = text.replace(attachment.redirectUrl, encodeURI(attachment.key));
-    }
-
-    let title = serializeFilename(document.title) || "Untitled";
-
-    const extension = format === FileOperationFormat.HTMLZip ? "html" : "md";
-
-    title = safeAddFileToArchive(zip, `${title}.${extension}`, text, {
-      date: document.updatedAt,
-      comment: JSON.stringify({
-        createdAt: document.createdAt,
-        updatedAt: document.updatedAt,
-      }),
-    });
-
-    if (doc.children && doc.children.length) {
-      const folder = zip.folder(path.parse(title).name);
-
-      if (folder) {
-        await addDocumentTreeToArchive(folder, doc.children, format);
-      }
-    }
-  }
-}
-
-/**
- * Adds the content of a file in remote storage to the given zip file.
- *
- * @param zip JSZip object to add to
- * @param key path to file in S3 storage
- */
-async function addImageToArchive(zip: JSZip, key: string) {
-  try {
-    const img = await getFileByKey(key);
-
-    // @ts-expect-error Blob
-    zip.file(key, img, {
-      createFolders: true,
-    });
-  } catch (err) {
-    Logger.error("Error loading image attachment from S3", err, {
-      key,
-    });
-  }
-}
-
-/**
- * Adds content to a zip file, if the given filename already exists in the zip
- * then it will automatically increment numbers at the end of the filename.
- *
- * @param zip JSZip object to add to
- * @param key filename with extension
- * @param content the content to add
- * @param options options for added content
- * @returns The new title
- */
-function safeAddFileToArchive(
-  zip: JSZip,
-  key: string,
-  content: string | Uint8Array | ArrayBuffer | Blob,
-  options: JSZip.JSZipFileOptions
-) {
-  // @ts-expect-error root exists
-  const root = zip.root;
-
-  // Filenames in the directory already
-  const keysInDirectory = Object.keys(zip.files)
-    .filter((k) => k.includes(root))
-    .filter((k) => !k.endsWith("/"))
-    .map((k) => path.basename(k).replace(/\s\((\d+)\)\./, "."));
-
-  // The number of duplicate filenames
-  const existingKeysCount = keysInDirectory.filter((t) => t === key).length;
-  const filename = path.parse(key).name;
-  const extension = path.extname(key);
-
-  // Construct the new de-duplicated filename (if any)
-  const safeKey =
-    existingKeysCount > 0
-      ? `${filename} (${existingKeysCount})${extension}`
-      : key;
-
-  zip.file(safeKey, content, options);
-  return safeKey;
-}
-
-/**
- * Write a zip file to a temporary disk location
- *
- * @param zip JSZip object
- * @returns pathname of the temporary file where the zip was written to disk
- */
-async function archiveToPath(zip: JSZip): Promise<string> {
-  return new Promise((resolve, reject) => {
-    tmp.file(
-      {
-        prefix: "export-",
-        postfix: ".zip",
-      },
-      (err, path) => {
-        if (err) {
-          return reject(err);
-        }
-        zip
-          .generateNodeStream({
-            type: "nodebuffer",
-            streamFiles: true,
-          })
-          .pipe(fs.createWriteStream(path))
-          .on("finish", () => resolve(path))
-          .on("error", reject);
-      }
-    );
-  });
-}
-
-export async function archiveCollections(
-  collections: Collection[],
-  format: FileOperationFormat
-) {
-  const zip = new JSZip();
-
-  for (const collection of collections) {
-    if (collection.documentStructure) {
-      const folder = zip.folder(serializeFilename(collection.name));
-
-      if (folder) {
-        await addDocumentTreeToArchive(
-          folder,
-          collection.documentStructure,
-          format
-        );
-      }
-    }
-  }
-
-  return archiveToPath(zip);
-}
-
-/**
- * Converts the flat structure returned by JSZIP into a nested file structure
- * for easier processing.
- *
- * @param paths An array of paths to files in the zip
- * @returns
- */
-export function zipAsFileTree(
-  zip: JSZip,
-  /** The maximum number of files to unzip */
-  maxFiles = 10000
-) {
-  let fileCount = 0;
-  const paths = Object.keys(zip.files).map((filePath) => {
-    if (++fileCount > maxFiles) {
-      throw ValidationError("Too many files in zip");
-    }
-
-    return `/${filePath}`;
-  });
-  const tree: FileTreeNode[] = [];
-
-  paths.forEach(function (filePath) {
-    if (filePath.startsWith("/__MACOSX")) {
-      return;
-    }
-
-    const pathParts = filePath.split("/");
-
-    // Remove first blank element from the parts array.
-    pathParts.shift();
-
-    let currentLevel = tree; // initialize currentLevel to root
-
-    pathParts.forEach(function (name) {
-      // check to see if the path already exists.
-      const existingPath = find(currentLevel, {
-        name,
-      });
-
-      if (existingPath) {
-        // The path to this item was already in the tree, so don't add again.
-        // Set the current level to this path's children
-        currentLevel = existingPath.children;
-      } else if (name.endsWith(".DS_Store") || !name) {
-        return;
-      } else {
-        const newPart = {
-          name,
-          path: filePath.replace(/^\//, ""),
-          title: deserializeFilename(path.parse(path.basename(name)).name),
-          children: [],
-        };
-
-        currentLevel.push(newPart);
-        currentLevel = newPart.children;
-      }
-    });
-  });
-
-  return tree;
-}