Rechargeable organic batteries show great potential as a low-cost, sustainable and mass-producible alternatives to current transition-metal-based cells; however, serious electrode dissolution issues and solubilization of organic redox intermediates (shuttle effect) have plagued the capacity retention and cyclability of these cells. Here we report on the use of a metal–organic framework (MOF) gel membrane as a separator for organic batteries. The homogeneous micropores, intrinsic of the MOF-gel separator, act as permselective channels for targeted organic intermediates, thereby mitigating the shuttling problem without sacrificing power. A battery using a MOF-gel separator and 5,5′-dimethyl-2,2′-bis-p-benzoquinone (Me2BBQ) as the electrode displays high cycle stability with capacity retention of 82.9% after 2,000 cycles, corresponding to a capacity decay of ~0.008% per cycle, with a discharge capacity of ~171 mA h g−1 at a current density of 300 mA g−1. The molecular and ionic sieving capabilities of MOF-gel separators promise general applicability, as pore size can be tuned to specific organic electrode materials. The use of MOF-gel separators to prevent side reactions of soluble organic redox intermediates could lead to the development of rechargeable organic batteries with high energy density and long cycling life.