Look into using Tags to identify each department. With a Tag added to the category of each transaction, then a report subtotaled by Tag will handle what you want.
Can you provide an example (link) to visualize the concept. Having a hard time understanding the hierarchy and structure.
The largest department will be food. This will have income for purchasing the food (finished product) and the expense in making the finished product. Do I create this department as in income when creating categories?
Thank you in advance.