A system for preparing patient-specific compounded medication doses is disclosed. The system includes a computerized medication compounding workstation configured to receive a patient-specific compounded medication dose order over a network and retrieve an electronically stored protocol having a set of steps to prepare a patient-specific compounded medication dose specified by the patient-specific compounded medication dose order. The example workstation is also configured to display, on a graphical user interface to a pharmacy operator, information related to the set of steps for preparing the patient-specific compounded medication dose and receive input related to the preparation of the patient-specific compounded medication dose including at least medication information scanned from at least one source medication container and a digital image from a digital camera. The workstation verifies completion for each step before allowing the pharmacy operator to move to a next step to prepare the patient-specific compounded medication dose.