The thesis presents the definition and design of the Attitude and Orbit Control System (AOCS) suite for SmallSat spacecraft, with a specific focus on addressing the challenges posed by Parasitic Torques generated by electric propulsion system. The work is focused on handling the AOCS control loop level of the disturbances generated by misalignment and uncertainties of the thrust vector and the relative impacts at the system level. A trade-off analysis is conducted to evaluate the effectiveness of the Thruster Pointing Mechanism (TPM) versus a cold gas Reaction Control System (RCS). Considering a deep space mission scenario, based on a 12U CubeSat equipped with an electric propulsion, an algorithm for handling the TPM in order to offset the Internal Momentum is developed.