The Journal Manager is responsible for managing the publishing system. This does not involve any advanced technical skills, but entails filling out templates and uploading files. The Journal Manager does the Setup for the journal, and enrolls the Editors, Section Editors, Copyeditors, Layout Editors, Proofreaders, and Reviewers. Alternately, names and emails of Reviewers, if they already exist in another database, can be imported into the system, through the Import People function under Import/Export Data. The Journal Manager also has access to the journal's other management systems, and can create new Sections for the journal, edit the default set of Emails the system uses, manage the Reading Tools that are available with this journal, and see to the Journal Statistics the system can generate.

Note that although the Journal Manager role is ostensibly a per-journal role, journal managers should generally be considered system-wide trusted users, as they have the ability to assume the identities of other users who may be enrolled in other journals.