A pharmaceutical compounding system having automated micro-dosing capability and using exchangeable source containers containing respective drugs, the system comprising an automated capsule-filling machine configured for compounding: an interface configured for receiving of prescription information for particular patients; and a dispensing head containing a solid-form drug; wherein said drug can be dispensed from said dispensing head by said machine such that the drug's active pharmaceutical ingredient (API) alone can be accurately dosed; and wherein the dispensing head is part of a set of multiple dispensing heads configured for compounding with said system.