Understanding the poisoning and deactivation pathways of metal–organic frameworks (MOFs) is an essential goal to boost their application as robust and efficient catalysts in chemical transformations relevant to industrial processes. Herein, the acetalization reaction of benzaldehyde with methanol was investigated by using [Cu3(BTC)2] (BTC=1,3,5‐benzenetricarboxylate) as a catalyst. The reaction was performed under batch and continuous flow conditions, and the conversion of benzaldehyde into 1,1‐dimethoxytoluene proceeded efficiently in the presence of a modest amount of water. Nevertheless, a drastic reduction in the catalytic activity was observed after recycling the MOF for repetitive batch experiments and after prolonged continuous flow tests. Pore clogging of the MOF and partial crystal‐structure modifications, gathered from XRD and pore analyses, suggested grinding the catalyst prior to application; the ground catalyst showed a considerable enhancement in catalytic performance.