Deep-space missions will be performed in the future by several stand-alone CubeSats. For limited budget reasons, these spacecraft need to follow operational compliant trajectories: transfers with an alternation of coasting and thrusting periods imposed at pre-defined time instants, the duty cycles. Traditional trajectory optimization algorithms exhibit convergence problems when handling this kind of discontinuous constraints. In this work, an efficient and robust indirect method to compute operational compliant trajectories is formulated through the imposition of coasting arcs as interior-point constraints. Results show that the computed trajectories are similar to the optimal ones with no operational constraint, both in terms of thrusting profile and propellant mass.