In this work, the Li‐ion insertion mechanism in organic electrode materials is investigated through the lens of atomic‐scale models based on first‐principles theory. Starting with a structural analysis, the interplay of density functional theory with evolutionary and potential‐mapping algorithms is used to resolve the crystal structure of the different (de)lithiated phases. These methods elucidate different lithiation reaction pathways and help to explore the formation of metastable phases and predict one‐ or multi‐electron reactions, which are still poorly understood for organic intercalation electrodes. The cathode material dilithium 2,5‐oxyterephthalate (operating at 2.6 V vs. Li/Li+) is investigated in depth as a case study, owing to its rich redox chemistry. When compared with recent experimental results, it is demonstrated that metastable phases with peculiar ring‐ring molecular interactions are more likely to be controlling the redox reactions thermodynamics and consequently the battery voltage.