How to Merge PDFs and Keep Their Bookmarks

Updated 2026-11-04

A PDF’s bookmarks are stored separately from its pages, so a merge that only copies the pages leaves the navigation behind. Combine a few chapters or reports that each had a clickable outline and you can end up with one long document that has no table of contents in the sidebar at all.

This guide merges PDFs in your browser and carries every file’s bookmarks over. Page numbers are shifted for you, and an optional top-level bookmark per file keeps the result easy to navigate even when some of the files had no bookmarks. Files are processed locally and never uploaded.

Use the tool: Merge PDF Files Online

Merge PDFs and keep the bookmarks, step by step

You need at least two files. The default settings already do what most people want:

Open the "Merge PDFs" tool and click "Add PDF Files". Choose two or more PDFs - they are read locally, never uploaded
Drag the items in the list into the order you want; the merged document follows this order. Select a file on the left to preview it
Check the two options: "Keep bookmarks from each file" and "Add a top-level bookmark per file". Both are on by default
Click "Start Merge". The result downloads as merged_document.pdf
Optionally open the merged file with "Open PDF" to check and tidy the outline (see the last section)

What happens to the bookmarks

Each file’s bookmark tree is copied and its page numbers are shifted by the number of pages that come before that file. If the first file has 10 pages, a bookmark that pointed to page 3 of the second file now points to page 13 - nothing to recalculate by hand.

With "Add a top-level bookmark per file" on, every source file becomes a top-level bookmark named after the file (without .pdf) that jumps to the file’s first page, with the file’s own bookmarks nested underneath. A file that has no bookmarks still gets this entry, so every source stays reachable from the sidebar.

With that option off, the files’ bookmarks are listed one after another at the top level in merge order, and a file without bookmarks adds nothing. The grouping option depends on "Keep bookmarks from each file": if that one is off, the merged PDF has no bookmarks at all.

Which setting should you choose?

Combining separate documents - reports, invoices, contracts, scans: keep both options on. The file names become the first level of the outline so you can jump from one document to the next, and scans without bookmarks still get one entry each.

Joining chapters of a single book where each file already starts with its own chapter title: turn "Add a top-level bookmark per file" off to get one flat outline in reading order instead of an extra level of file names.

Check and tidy the merged outline

Open the merged file with "Open PDF" and look at the Bookmarks panel. Click an entry to jump to its page in the preview. Hover over an entry to reveal the pencil ("Edit bookmark") - handy for renaming file-level bookmarks to something friendlier than the file name - and drag entries to reorder or nest them. Click "Save PDF" to download the tidied file.

Click a few entries from each source file and make sure they land on the right pages before you delete the originals.

FAQ

Do I lose the bookmarks when I merge PDFs?

Not with this tool as long as "Keep bookmarks from each file" is on, which is the default. Each file’s outline is carried over and its page numbers are shifted automatically. Switch the option off and the merged file has no bookmarks.

What happens to files that have no bookmarks?

With "Add a top-level bookmark per file" on, they still get one bookmark named after the file that points to their first page. With it off, they simply contribute no bookmarks.

What if one file’s bookmarks are missing from the merged PDF?

The merge carries on even if a file’s outline cannot be read; that file then has no bookmarks of its own. Open the merged PDF in the bookmark editor and add the missing ones with "Add bookmark".

Can I change the file order after merging?

The order is fixed when you click "Start Merge", so arrange the list first. The simplest way to change it afterwards is to merge again from the original files.