The Cluster mission comprises four 'identical' satellites devoted to the study of the Earth's magnetosphere. For accurate differential measurements, it is important to maintain a precise understanding of instrument performance. Hence, for Cluster and future multi-spacecraft missions, an effective method of in-orbit monitoring and optimisation of detector behaviour is essential. This is particularly challenging in the case of microchannel plates (MCPs), especially in the situation where, because of lifetime considerations, no scrubbing of the plates was performed prior to launch. This paper explores just this problem in the case of the Cluster-PEACE sensors where the problem is made yet more difficult since mass and power constraints severely limited the amount of diagnostic data available from the instrument - in particular, no pulse height information is directly available. We describe here a technique that lets us evaluate the degradation of the MCPs in space and optimise the operation of the instrument to provide consistent performance. Utilising data from the two sensors on each satellite from various regions of space and coupling with ground characterisation/calibration data, normalised pulse height distributions are indirectly extracted. Although the general behaviour is as expected, the performance shows considerable differences between the different sensors. The results also differ considerably in detail from lifetime tests carried out with a representative MCP on the ground.