The charge-storage mechanism in manganese dioxide (MnO2)-based electrochemical supercapacitors was investigated and discussed toward prepared MnO2 microstructures. The preparation of a series of MnO2 allotropic phases was performed by following dedicated synthetic routes. The resulting compounds are classified into three groups depending on their crystal structures based on 1D channels, 2D layers, or 3D interconnected tunnels. The 1D group includes pyrolusite, ramsdellite, cryptomelane, Ni-doped todorokite (Ni-todorokite), and OMS-5. The 2D and 3D groups are composed of birnessite and spinel, respectively. The prepared MnO2 powders were characterized using X-ray diffraction, scanning electron microscopy, the Brunauer−Emmett−Teller technique, cyclic voltammetry (CV), and electrochemical impedance spectroscopy. The influence of the MnO2 microstructure on the electrochemical performance of MnO2-based electrodes is commented on through the specific surface area and the electronic and ionic conductivities. It was demonstrated that the charge-storage mechanism in MnO2-based electrodes is mainly faradic rather than capacitive. The specific capacitance values are found to increase in the following order: pyrolusite (28 F·g−1) < Ni-todorokite < ramsdellite < cryptomelane < OMS-5 < birnessite < spinel (241 F·g−1). Thus, increasing the cavity size and connectivity results in the improvement of the electrochemical performance. In contrast with the usual assumption, the electrochemical performance of MnO2-based electrodes was not dependent on the specific surface area. The electronic conductivity was shown to have a limited impact as well. However, specific capacitances of MnO2 forms were strongly correlated with the corresponding ionic conductivities, which obviously rely on the microstructure. The CV experiments confirmed the good stability of all MnO2 phases during 500 charge/discharge cycles.