Non-native structures have more open structure with less stable bulk formation energy compared to their native structure and hence, non-native structured cathodes are expected to generate higher discharge potential and better lithium mobility. However, non-native structures are limited in stability, which can be enhanced by scaffolding with native structure. We synthesize highly crystalline non-native Ramsdellite MnO2 (r/NN1–MnO2) and gradually thermal phase transform to native Pyrolusite MnO2 (β/N–MnO2), intimately interfaced (r/NN1–MnO2)/(β/N–MnO2) intergrowth intermediate structures are realized. As the temperature increases, the ratio of r/NN1–MnO2 to β/N–MnO2 in intergrowth structure decreases, so does the discharge potential and lithium mobility. The wider discharge plateau for intergrowth structures is rationalized using density functional simulations followed by statistical averaging to account for interfacial intercalation sites with greater stability. Improved capacity retention for intergrowth structure is due to the higher structural stability and available free volume, where the presence of native structure acts as a stabilizing element. Electrochemical impedance spectroscopy correlates faster transport in the intergrowth structure with higher percentage of non-native phase with wider 2 × 1 channel compared to native phase with narrow 1 × 1 channel. The insights generated from this study have broad implications for interface engineering in multicomponent electrodes such as Li-rich-NMC oxides. © 2019 Elsevier B.V.