Shared content items are migrated between accounts on a content management system. Users store content items synchronized between one or more client devices and the content management system. A user may have multiple accounts including personal and organization accounts. Content items may be shared with accounts belonging to other users to enable those other users to view or manipulate the content items. A user initiates a migration of content items between accounts of different categories via a user interface, e.g., by dragging and dropping a folder from one account to another. The content management system recognizes that the user has deleted the folder from the user's first account and determines that an identical folder has been created in another account belonging to the same user. In response the content management system joins the second account to the shared folder, and removes the first account from the shared folder.