Flexible and green energy storage devices have a wide range of applications in prospective electronics and connected devices. In this study, a new eco-friendly bilayer separator and primary and secondary paper supercapacitors based on manganese dioxide (MnO2)/carbon black (CB) are developed. The bilayer separator is prepared via a two-step fabrication process involving freeze–thawing and nonsolvent-induced phase separation. The prepared bilayer separator exhibits superior porosity of 46%, wettability of 46.5°, and electrolyte uptake of 194% when compared with a Celgard 2320 trilayer separator (39%, 55.58°, and 110%). Moreover, lower bulk resistance yields a higher ionic conductivity of 0.52 mS cm–1 in comparison to 0.22 mS cm–1 for the Celgard separator. Furthermore, the bilayer separator exhibits improved mean efficiency of 0.44% and higher specific discharge capacitance of 13.53%. The anodic and cathodic electrodes are coated on a paper substrate using MnO2/CB and zinc metal-loaded CB composites. The paper supercapacitor demonstrates a high specific capacitance of 34.1 mF cm–2 and energy and power density of 1.70 μWh cm–2 and 204.8 μW cm–2 at 500 μA, respectively. In summary, the concept of an eco-friendly bilayer cellulose separator with paper-based supercapacitors offers an environmentally friendly alternative to traditional energy storage devices.