Multi-microscopy offers significant benefits to the understanding of complex materials behaviour by providing complementary information from different properties. However, some characterisations may strongly influence other measurements in the same workflow. To acquire reliable and valid datasets, optimising multi-microscopy procedure is necessary. In present work, we studied the influence of the measurement order on the quality of multi-microscopy datasets. Multi-microscopy incorporating tunnelling current AFM (TUNA), electron backscatter diffraction (EBSD), and cathodoluminescence (CL) on a polycrystalline solar cell absorber, Cu(In,Ga)S