Where apps hide your files
Zotero keeps your library in one visible folder in your home directory, so this is one of the easier hunts. The database is zotero.sqlite and your attached PDFs are in storage.
On macOS, Zotero's documentation gives the default data directory as:
/Users/<username>/Zoterowhich is ~/Zotero. It is a normal visible folder in your home folder. Open it from Terminal:
open ~/ZoteroYou may have changed it, or an older setup may use another place. The reliable way to find your current folder is inside Zotero: choose Zotero > Settings (Preferences in Zotero 6 and earlier), open the Advanced pane and scroll to Files and Folders. Under Data Directory Location you see the current path, and the Show Data Directory button opens it in Finder. If you cannot open Zotero, search for zotero.sqlite by name: the folder holding it is the data directory.
| Item | What it is |
|---|---|
zotero.sqlite | The main database: item metadata, notes and tags. |
storage | Subfolders with 8-character names (such as N7SMB24A) holding your attached files. Linked files are not copied here. |
zotero.sqlite-wal, zotero.sqlite-shm | Temporary files used while Zotero is open. |
zotero.sqlite.bak, zotero.sqlite.1.bak | Automatic backups of the database, made at most once a day by default. |
fulltext.sqlite | Full-text search index. Zotero does not back it up, because it can be recreated automatically. |
locate, logs, pipes, styles, translators | Folders created at startup. |
Those descriptions are from Zotero's own page on the data directory. The eight-character folder names in storage are the attachments' item keys, not titles, so a PDF will sit at a path like storage/ABCD1234/<original file name>.pdf. To find a paper, search for its file name, not its folder.
Do not copy individual files out of storage to share a library, because the database is what connects them to titles, tags and notes. For references, use File > Export Library…, or right-click a collection and choose Export…, which writes formats such as RIS or BibTeX. For a full copy of a library, copy the whole data directory.
Zotero's guidance is to close Zotero first, then copy the whole data directory, including zotero.sqlite, storage and the other folders. Keep zotero.sqlite-wal alongside zotero.sqlite if you copy the database. Zotero says not to treat export as a backup.
Two cautions from Zotero's page. If file syncing is set to download files as needed, some attachments may not exist locally, so they would be missing from a copy of the folder. On the Mac you back up, set file downloads to at sync time in the Sync pane so every attachment is on disk. And the automatic .bak files sit in the same folder as the database, so they protect against a bad database, not a dead disk. Time Machine or another full-system backup covers the rest.
Zotero's settings let you pick a custom location, but Zotero does not move or copy your data for you:
storage, styles and the rest).Point Zotero at the folder that holds zotero.sqlite and storage, not at storage itself. Zotero's own settings guide calls the default "the best location for most users".
Zotero's documentation calls a cloud storage folder, the kind Dropbox or iCloud Drive syncs, extremely unsafe for the data directory, because those services do not honour the database's locks. It also says never to share one database between computers over a network drive, and that an external disk is usually safe but can corrupt the database if it unmounts while Zotero is open. If you want your library on several Macs, use Zotero's own sync instead.
To see how big the library has grown, without opening anything:
du -sh ~/Zotero ~/Zotero/storageMost of the weight is usually storage, the attachments. If the total looks too small for the library you remember, you may be looking at the wrong folder: Zotero's page on missing data lists a data directory set to the wrong location as one of the usual causes of a library that looks empty. Compare against the path in settings, and look for any other folder containing a zotero.sqlite file before you assume data is lost. Keep the .bak files: each is a full copy of the database, so they take about as much space as zotero.sqlite, and they are your fallback if it is damaged.
If you attach files as links instead of storing copies, they stay where they were, outside the data directory. The Linked Attachment Base Directory setting, in the same Files and Folders section, only helps Zotero find those files on other computers with different paths. It does not decide where anything is stored.
~/Zotero is an ordinary folder outside ~/Library, so Finder and Spotlight searches do reach it. What trips people up is the layout: each PDF sits in its own folder named with a key, so a result tells you little about which item it belongs to. Attachments that file syncing has not downloaded yet are not on disk at all, and linked files live wherever you left them.
Typing a paper's file name into Everywhere finds its PDF inside storage and shows the path, and typing zotero.sqlite finds the database from anywhere. ⌘↵ reveals the match in Finder, and the path you see tells you which storage folder it came from. If you moved the data directory into Documents or onto an external drive, Everywhere covers it once it has Full Disk Access. It matches names only, so it cannot search the text of papers or the titles in your Zotero library.
By default ~/Zotero, per Zotero's documentation. In Zotero > Settings > Advanced, the Files and Folders section shows the current path and a Show Data Directory button.
In subfolders of the storage folder in the data directory, each named with an 8-character key. Linked files are not copied there and stay where you left them.
Quit Zotero and copy the whole data directory, keeping zotero.sqlite-wal with the database. Zotero says not to use export as a backup.
Zotero advises against it, because cloud-synced folders can corrupt the database. Use Zotero's own sync to share a library between computers.
Everywhere keeps track of every file on your Mac — including the folders Spotlight hides and drives you have unplugged. Free for a day, then $19 once.
Version 2.20.3 · macOS 13+ · 4.7 MB · notarised