This paper presents the design, development and implementation of a bio-inspired fault diagnosis scheme applied to a cold gas based spacecraft prototype. The proposed framework relies on the Artificial Immune System metaphor (AIS) with the goal of monitoring the health of the spacecraft by detecting subsystem upset conditions such as actuator malfunctions. A non-linear dynamic inversion (NLDI) baseline controller has been developed and implemented for attitude control of the spacecraft. The performance of the proposed health monitoring scheme is determined by analyzing the system response under different actuator failures and the results show acceptable performance in terms of high detection rate and low false alarms. The application of this artificial intelligent based scheme to aerospace systems will provide a high impact on space exploration by increasing mission protection and performance.