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How To Join PDFs And Maintain Bookmarks?

Merging scanned chapters into a single PDF for a fanfic archive, but my manually added bookmarks keep disappearing. What's the best tool to preserve them all?
2026-07-29 21:26:16
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7 Answers

Best Answer
sonoko091901
sonoko091901
If you need to keep your bookmarks when merging PDF files, any decent PDF editor, in their ‘combine’ or ‘merge’ tool, should have a checkbox to enable the retaining of existing bookmarks. Depending on the complexity of your outlines, it might be useful to use tools like Adobe Acrobat or even open-source solutions like PDFsam to rearrange and even to add new bookmarks after merging files. I must say, I’m grateful to the author of the novel ‘Naked Pages’ for having published it as a complete volume of a single PDF file, ‘Naked Pages’ is a complex trippy plot that jumps between a writer’s drafts and reality, and it was nice reading it as one file with proper chapter markers to a page.
2026-08-04
Ramon Hulloa
Ramon Hulloa
Philosophy: Merge PDFs to have Whole Stories. Right now we have fragmented stories with scattered chapters and scattered lore entries. By merging PDFs and keeping the bookmarks intact, you are engaging in a form of curation and creating whole stories out of your fragmented stories.

The bookmark tree becomes the spine of the PDF, telling a story about how we have read a document. The PDF becomes more organized and starts to resemble a physical book that has been curated and constructed rather than a haphazard accumulation of documents that were thrown together by chance.
2026-08-01
Melissa
Melissa
That would be overcomplicating things for 90% of users. Adobe Acrobat Reader DC (the free version) can combine PDF files using Tools > Combine Files. Just add your files, click on Combine, and the resulting PDF will have a document outline that corresponds to the files’ basic structure. I did not test any more than that. For simple ebook or document structures with chapter headings, this will likely work just fine. Next stop: specialty tools – if you need them.

Why would you install more software when you could try the free tool from the creators of PDF first? If it doesn’t work, then you can start looking at the many specialty tools available. I found that starting simple worked for me!
2026-08-01
Abigail
Abigail
I have found that there are a few ways to merge PDFs with bookmarks. First, I recommend using Adobe Acrobat as it is the most straightforward way to do this. Under the tool, select “Combine Files” and add the PDFs that you wish to merge. Make sure the option to “Include bookmarks” is selected before you complete the process. Next, I recommend using “PDF-XChange Editor” as it is a very lightweight editor that allows you to drag and drop files in order to merge them while preserving bookmarks. Finally, if you are looking for free alternatives, “PDFsam Basic” is a decent merge tool, although you will have to manually reorganize the merged PDF’s bookmarks afterwards. It is always a good idea to review the merged file to make sure that everything has merged as expected.
2026-08-03
Nolan
Nolan
Even better, when combining PDF files together without losing bookmarks, Adobe Acrobat is often a good solution for this problem as it supports the merging of PDF files with bookmarks intact. To merge files, simply drag and drop the files into the “Combine Files” window, select “Include Bookmarks” and click “Merge”.

On the Mac, Preview can combine PDF files but will neglect to include any bookmarks. One program that will include bookmarks when combining PDFs on the Mac is PDF Expert (by Readdle). I have also included PDFtk Builder (which is available for Mac and also for other OS) as an option for those looking to combine PDFs in bulk, though I warn that the program is somewhat cumbersome to use. After merging your PDF files, make sure to open them and verify the links to ensure that all bookmarks were correctly incorporated. It is not uncommon for the process of combining PDFs that contain many intricate bookmarks to result in some bookmarks becoming “disjointed” or in need of cleaning up in PDFescape to reorganize.
2026-08-03

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