Can I save my PDFs to a single folder?

I am just learning to use Zotero. I have figured out how to add ZotFile and rename PDFs from parent metadata. I notice that these PDFs, when imported and renamed from my "Downloads" folder, are sorted into folders with random 8-digit names within "C:\Users\Sarah\Zotero\storage". For example, "SerratX et al_2019_PLoS Genet.pdf" is in "C:\Users\Sarah\Zotero\storage\6YD4PSYF\". Is it possible to have my PDFs in a single folder (like C:\Users\Sarah\Zotero\storage\") so I can search more quickly through my list of PDFs by sorting all files alphabetically? This is something I used to do in Mendeley and it was very convenient. Alternatively, can I make it so the final folder name (e.g., "6YD4PSYF") is informative (e.g., renamed from parent metadata)?
  • Additionally, I am playing around with adding notes that I want to save with the PDFs. So I would make Word Document Titled "Serrat_2019_Notes.docx". I used "Attach stored copy of a file" to like that document to the paper, and this created a NEW folder in storage: "C:\Users\Sarah\Zotero\storage\JWLP7VLC\". Over time this is going to make the "storage" folder a mess of folders whose names are gibberish. Is there a more efficient way to sort and store PDFs, supplemental files, and word docs in storage? It's very neatly organized in the app, but what if I want to easily find and access these files just from the folder?
  • to *link that document to the paper
  • edited March 19, 2021
    The basic idea of Zotero is that you don't touch your PDF files in their folders-- that's what Zotero is for, with much better search & filter options than your file system.

    If you do really want them in a human-readable folder structure, you have two main options:
    1. You can just set up a saved search in Windows within the storage folder for PDFs -- that will give you all PDFs in a single folder: (see e.g. for saved searches)
    2. You can set up ZotFile to move files as linked files to a different folder, where it is also able to add a folder structure. Note, though, that linked files aren't synced by Zotero and not available e.g. via the iOS app.
  • Thanks for the answer! I will think if I want to do that or just accept this formatting.
  • edited May 13, 2021
    This is a hard to decide question for a users. Have no human readable file format for PDFs or no access via iOS. One alternative could be to use Zotfile to store PDFs to defined folder and then use an iOS PDF reader capable of WebDAV to access that folder.

    I have Zotfile installed and set "Location of Files" to a WebDAV volume. But no files are stored at the defined location. Having a hard time to tell what I am doing wrong or how to make this work.

    Custom Location : /Volume/WebDAVname/zotero/PDF (shows with green checkmark)
    Use subfolder defined by: /%w/%y (while that has an i for additional info I assume, clicking the "i" does nothing) so I am not sure what my options are with that field.

    Maybe Zotero > Preferences > Advanced > Files and Folders
    and Zotero > Tools > ZotFile Preferenecs > Locations and Files
    are in conflict?

    How do I know which setting is being followed? From my understanding both options exlude each other so it is very odd to have them both available at the same time. Again, I am very new to Zotero and documentation is hard to follow and more questions pop up in my mind than I find answers currently.
  • First, just to be clear -- the file formats and names Zotero uses are of course perfectly human-readable. This is only the folder structure/filepaths.

    Then, the ZotFile preferences are what's relevant here. The Zotero files and folders preferences do not actually contradict them: One of them is for the data directory, which doesn't just include stored files, but also the database; the other one is for relative links, which can complement files linked via ZotFile when working on multiple computers.

    ZotFile documentation, including what the various wildcards do, is here:

    To test whether ZotFile is working and generally able to move files, try manually moving an attached PDF using Manage Attachments --> Rename attached files.
  • @adamsmith thank you for your patience and elaborating on some aspects. Things are actually working as expected. I was unaware I need to do the renaming part for the file to be stored in the location defined in ZotFile Preferences.

    This is awesome. Starting to get the idea slowly but surely.
  • ZotFile should do this automatically in many scenarios (esp. when importing metadata with attached PDF from the web) but it doesn't automatically move/rename files when they were added as PDFs and Zotero automatically retrieves the metadata
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