In the present work, we provide insight in the degradation mechanism of Li-organic batteries utilizing the cathodes based on the NDI-С2 polyimide formed by naphthalene-1,4,5,8-tetracarboxylic acid dianhydride and ethylene diamine. The introduction of the C2H4 spacers between the imide units in the polymer backbone makes it stable with respect to the reductive fragmentation upon lithiation. However, NDI-С2 features conformationally flexible linear polymer chains, which can be converted under lithiation into very compact and energetically favorable zigzag-type structures. This conversion can be almost irreversible, since unfolding and delithiation of the zigzag-type architectures is strongly hampered by the steric and kinetic factors. The formation of “frozen” lithiated states of the redox-active material explains the severe capacity fade under cycling. Since the polymer chain mobility is largely enhanced when the material undergoes swelling, the solvent has a strong impact on the degradation kinetics. In particular, we confirmed that using ether-based solvents delivers more stable devices compared to the batteries assembled with standard carbonate electrolyte. As the main conclusion, our findings strongly suggest that conformationally-flexible redox-active polymers offer limited promise with respect to the battery applications. On the contrary, more attention should be paid to the use of rigid low molecular weight or polymer-based electroactive structures as advanced cathode and anode materials for all organic-based energy storage devices.