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I've found lots of info on decrypting PDF files, but none on encrypting them. What tool can do this for me?

Edit: There are two good answers below, but in my specific case the PDF was a scan, not a document that I'd created.

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Use pdftk. From its man page:

Encrypt a PDF using 128-Bit Strength (the Default) and Withhold All Permissions (the Default) 

$ pdftk [mydoc].pdf output [mydoc.128].pdf owner_pw [foopass]

Same as Above, Except a Password is Required to Open the PDF 

$ pdftk [mydoc].pdf output [mydoc.128].pdf owner_pw [foo] user_pw [baz]

Same as Above, Except Printing is Allowed (after the PDF is Open) 

$ pdftk [mydoc].pdf output [mydoc.128].pdf owner_pw [foo] user_pw [baz] allow printing

pdftk has a lot of other uses as well and is worth installing if one works extensively with PDF files. To quote from the write-up in Synaptic:

If PDF is electronic paper, then pdftk is an electronic stapler-remover, hole-punch, binder, secret-decoder-ring, and X-Ray-glasses. Pdftk is a simple tool for doing everyday things with PDF documents. Keep one in the top drawer of your desktop and use it to:

  • Merge PDF documents
  • Split PDF pages into a new document
  • Decrypt input as necessary (password required)
  • Encrypt output as desired
  • Fill PDF Forms with FDF Data and/or Flatten Forms
  • Apply a Background Watermark
  • Report PDF on metrics, including metadata and bookmarks
  • Update PDF Metadata
  • Attach Files to PDF Pages or the PDF Document
  • Unpack PDF Attachments
  • Burst a PDF document into single pages
  • Uncompress and re-compress page streams
  • Repair corrupted PDF (where possible)
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    If you wish a GUI for pdftk, you can try pdfchain that works good. For the above needing, you can use the Concatenate tab, adding only one PDF, and settings permissions options and password.
    – Stefano
    Feb 26, 2013 at 22:27
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    The most recent release of pdfchain brings a number of enhancements but isn't available from the official repositories yet. You can install it via this PPA (maintained by the developers): launchpad.net/~pdfchain-team/+archive/ppa
    – Glutanimate
    Feb 27, 2013 at 10:33
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    I tried the first example with pdftk 1.44, and I could open the resulting PDF without a password using evince. Only after adding user_pw was the document actually protected.
    – Joey Adams
    Aug 8, 2013 at 20:43
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    @JoeyAdams owner_pw is intended to protect the pdf against modifications; the second example specifically adds user_pw to require a password to read the file.
    – carnendil
    Sep 5, 2017 at 17:43
  • If you just want a single password to open it, you can use pdftk [mydoc].pdf output [mydoc.128].pdf user_pw [baz], skipping the owner setting.
    – colan
    Mar 22, 2020 at 22:09
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If you use LibreOffice and export a document as PDF (Menu > File > Export as PDF), there's the option to set a password:

enter image description here

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  • Unfortunately my PDF is from a scan, but that would be a good general solution.
    – mfisch
    Feb 20, 2013 at 17:30
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    Shouldn't it still be possible since you can import images into LibreOffice and then export as PDF?
    – user25656
    Feb 20, 2013 at 17:36
  • I had a scanned document that the macOS Preview.app failed to encrypt correctly. Using LibreOffice to encrypt the PDF was the only way I was able to get this done, short of putting the doc on a linux server, installing pdftk and doing it on the CLI.
    – JinnKo
    Feb 16, 2018 at 11:29
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qpdf can encrypt and decrypt pdfs. And linearize them, too.

examples:

  • decryption:
    • qpdf --password='·······' --decrypt input.pdf output.pdf
  • encryption: 256bit AES

Link to qpdf online Manual

Ubuntu Launchpad PPA

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PDF Chain is an awesome tool for this. It is a GUI for pdftk

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One possible solution is to use jpdf Tweak.

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Master PDF Editor is a very good GUI for editing pdf also can encrypt. It also uses latest PDF standard. Used PDF Chain and Master PDF editor, both to encrypt a pdf, With PDF Chain the PDF outputed was larger and lost bookmarks, was almost double the size.

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