The Zotero desktop app is the primary way of using Zotero and offers complete functionality. When people talk about “Zotero”, they're almost always referring to the desktop app.

The Zotero web library is a complementary tool for accessing your Zotero data when you're away from your main computer or using a platform that can't run Zotero (locked-down institutional computers, some Chromebooks, etc.). The web library also allows you to share a Zotero library publicly with people who might not use Zotero.

A desktop app allows for vastly more functionality than a website. Here's an incomplete list of features that only the Zotero desktop app provides:

• A local database fully under your control, with optional syncing
• Fast, offline access to all your data — whereas the web library can only load a subset of your data at a time, the desktop app allows you to access and modify everything much faster
• Word, LibreOffice, and Google Docs plugins that let you insert citations and bibliographies directly from Zotero and keep them updated automatically
• A better experience when saving items from the Zotero Connector (+ other features)
• The ability to work with a large number of references — certain operations, like export and bibliography generation, are limited to 100 items in the web library for technical reasons
• Real windows that you can interact with via Cmd-Tab/Alt-Tab, resize, etc. — not just an interface within a single browser tab
• Local filesystem access — e.g., adding PDFs directly from your documents or creating links to files on the local disk
• Automatic retrieval of metadata for PDFs
• Find Available PDF to locate open-access versions of files
• Importing of references from a file or from other reference managers
• PDF full-text indexing (coming soon to web library)
• Advanced search and saved searches
• Retracted item notifications
• My Publications collection to share your work publicly
• CSL style editor
• Custom citation styles
• Unfiled items collection (coming soon to web library)
• Duplicate items collection and item merging
• Ability to create related items
• A user interface that adapts to the OS you're using
• An unrestricted plugin system that allows for many more features and further customization