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Self-discharge and chemically induced mechanical effects degrade calendar and cycle life in intercalation-based electrochromic and electrochemical energy storage devices. In rechargeable lithium-ion batteries, self-discharge in cathodes causes voltage and capacity loss over time. The prevailing self-discharge model centers on the diffusion of lithium ions from the electrolyte into the cathode. We demonstrate an alternative pathway, where hydrogenation of layered transition metal oxide cathodes induces self-discharge through hydrogen transfer from carbonate solvents to delithiated oxides. In self-discharged cathodes, we further observe opposing proton and lithium ion concentration gradients, which contribute to chemical and structural heterogeneities within delithiated cathodes, accelerating degradation. Hydrogenation occurring in delithiated cathodes may affect the chemo-mechanical coupling of layered cathodes as well as the calendar life of lithium-ion batteries.