This work presents the development of the navigation and control subsystems of a guidance, navigation and control (GNC) system for controlling an autonomous satellite, called chaser, equipped with a redundant manipulator. In the study, the capture operations of a target spacecraft and its stabilization are considered. The control function employs a combined control strategy: the chaser satellite actuators and the robotic arm joint motors are degrees of freedom of the same control plant. Robust control methods are used to cope with uncertain, nonlinear dynamics of the chaser and of the complete chaser–target stack after capture. The developed navigation function is based on active or passive electro-optical sensors (i.e., passive cameras and/or LIDARs) for the relative pose determination. A numerical simulator capable of representing the dynamics of the system (chaser, manipulator, target) in orbit is developed in the MATLAB/Simulink environment to validate the developed GNC algorithms. The simulation tool allows to thoroughly assess the GNC system performance, accounting for all the relevant external disturbances and error sources. The simulator interfaces with a synthetic image generator (i.e., PANGU) for relative navigation performance assessment. This paper presents the testing of the GNC system in two relevant In-Orbit Servicing (IOS) scenarios: (1) the servicing of a large GEO platform and (2) the servicing of a small satellite in Low Earth Orbit (LEO).