<p><strong>Electric propulsion drives are the future of long-life and high velocity space missions due to their superior mass efficiency and reliability. In particular, applied field magnetoplasmadynamic thrusters (AF-MPDTs) are the class of electric propulsion that have the largest thrust and could give humanity access to greater depths of our solar system. However, control aspects of AF-MPDTs have not yet been investigated and potential problems may arise if this type of thruster is used in low Earth orbit. We have shown that the interaction of the geomagnetic field with the strong AF-MPDT magnetic field will cause unwanted magnetic disturbance torques on a spacecraft while it is manoeuvring. The spacecraft will gain angular momentum per orbit from these disturbance torques, for all orbital inclinations in low Earth orbit. For a 100 kg spacecraft, the reaction wheels required for momentum management are too large from a mass perspective to compensate the magnetic disturbance torques. Using the analysis of magnetic disturbance torques, a control solution is proposed with an Extended Kalman Filter to estimate the magnetic disturbance and a PD (proportional derivative) based magnetorquer control law to compensate for the estimated disturbance as well as maintain the attitude orientation required for an orbital manoeuvre. We have shown that a spacecraft using an electromagnetic thruster can be controlled in low Earth orbit for inclinations above 50 degrees, but control characteristics become poor for near equatorial orbits due to controllibility issues relating to the homogeneity of the geomagnetic field and limitations on magnetorquer properties.</strong></p>