We present an advanced diagnostic system for in situ characterization of electric propulsion thrusters and ion beam sources. The system uses a high-precision five-axis positioning system with a modular setup and the following diagnostic tools: a telemicroscopy head for optical imaging, a triangular laser head for surface profile scanning, a pyrometer for temperature scanning, a Faraday probe for current density mapping, and an energy-selective mass spectrometer for beam characterization (energy and mass distribution, composition). The capabilities of our diagnostic system are demonstrated with a Hall effect thruster SPT-100D EM1.