Many of Zotero's features can be customized via the Zotero preferences. To access the Zotero preference window, either open the Zotero pane, click the actions menu button (the 'gear' icon) at the top of the left column and select the “Preferences…” option. Alternatively, in Firefox select “Add-ons” in the Tools menu, then select Zotero and click the “Options” button; in Zotero Standalone you can also access the preferences by selecting “Options” in the Edit menu.

The preferences in the preference window are divided over the following tabs:

• General - adjust appearance and set miscellaneous features.
• Sync - set your username, password and (if desired) WebDAV server for syncing.
• Search - turn full-text indexing of PDFs on and off and see relevant statistics.
• Export - specify how bibliographies are generated
• Cite - add and remove citation styles
• Proxies - configure proxy server settings (not available in Zotero Standalone)
• Shortcut Keys - configure keyboard shortcuts for Zotero
• Advanced - storage location, database integrity

In addition to the preferences shown in the Zotero preferences window, Zotero has a number of hidden preferences that only can be changed through the about:config page of Firefox or Zotero Standalone.