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You can do profit and loss reporting for a department by assigning a department to particular revenue and expense accounts that are for that department.
You need to have separate accounts for each department, and separate from the main business, in order for department level profit and loss reporting to work correctly.
When the department module is enabled you will see a "Department" selection button on the Profit & Loss Statement.
If you wish to report on the entire business then do not select a department when running the profit & loss statement.
The department profit and loss report has the details for the department printed at the top. The report calculates the profit and loss based on revenue and expense accounts that have been assigned to that department.