In the present work, we provide insight in the degradation mechanism of Li-organic batteries utilizing the cathodes based on the NDI-C2 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-C2 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.