Abstract Performance degradation is one of the key issues hindering direct methanol fuel cell commercialization, caused by different mechanisms interplaying locally and resulting in both temporary and permanent contributions. This work proposes a systematic experimental investigation, coupling in-situ diagnostics (electrochemical and mass transport investigation) with ex-situ analyses of pristine, activated and aged components (X-ray photoelectron spectroscopy and transmission electron microscopy), with an in-plane and through-plane local resolution. Such a combined approach allows to identify on one hand the degradation mechanisms, the affected components and the presence of heterogeneities; on the other hand, it allows to quantify the effect of the major mechanisms on performance decay. Thanks to a novel procedure, temporary (21 μV h−1) and permanent degradation (59 μV h−1) are separated, distinguishing the latter in different contributions: the effects of active area loss at both at anode (9 μV h−1) and cathode (31 μV h−1), mass transport issue (15 μV h−1) and membrane decay (4 μV h−1). The post-mortem analysis highlights the effect of degradation mechanisms consistent with the in-situ analysis and reveals the presence of considerable in plane and through plane heterogeneities in: particle size growth in catalyst layers, Pt/Ru and polymer content in catalyst and diffusion layers, Pt/Ru precipitates in the membrane.