Multilayered thin films of functional materials play an important role in many applications in nanotechnology. The intense and tuneable colours of some molecular materials allow for the development of a unique spectral fingerprint of each layer in thin film heterostructures. Herein, we report on electrochromic switching of bilayer thin films composed of Prussian blue (FeIIIFeII) and its orange-coloured (FeIICrIII) analogue. The films could be switched from green to orange by reducing the blue FeFe top layer. The distinct optical absorption spectra of the two layers allowed spectroelectrochemical measurements to probe the electrochemical activity of the individual layers during the switching of the Prussian blue layer. We found that for producing layers of equal optical density, the thickness of the layers had to be different due to a difference in oscillator strength for the metal-to-metal charge-transfer transition. The films used here had a thickness of 300 ± 70 nm and 30 ± 15 nm for the FeCr and FeFe sub-layers, respectively. The colouration efficiency was found to be 147.8 ± 0.8 cm2 C−1 for the multilayered film. These results show that it is possible to obtain bilayers of Prussian blues that, with a unique optical spectral fingerprint of each sub-layer, retain the electrochromic functionality and therefore enable layer-sensitive studies of charge-transfer processes in thin film heterostructures of multifunctional materials.