The use of System-on-Chip (SoC) solutions in the design of on-board data handling systems is an important step towards further miniaturization in space. However, the Total Ionizing Dose (TID) and Single Event Effects (SEE) characterization of these complex devices present new challenges that are either not fully addressed by current testing guidelines or may result in expensive, cumbersome test configurations. In this paper we report the test setups, procedures and results for TID testing of a SoC microcontroller both using standard C60o and low-energy protons beams. This paper specifically points out the differences in the test methodology and in the challenges between TID testing with proton beam and with the conventional gamma ray irradiation. New test setup and procedures are proposed which are capable of emulating typical mission conditions (clock, bias, software, reprogramming, etc.) while keeping the test setup as simple as possible at the same time.