Paper-based biofuel cells have the potential to serve as health monitoring devices for urinary glucose and volume by incorporating the fabricated electrodes into nursing diapers. In this study, we evaluate the output power and stability of a biofuel cell by combining 3D impedance measurement and admittance analysis. The 3D impedance-based analysis method can simultaneously detect changes in the overall electrode structure of the enzyme electrode and those in the quantity of active enzymes and mediators on the electrode surface. The biofuel cell electrodes were fabricated via screen-printing, using polydimethylglycidyl (poly-GMA)-modified MgO-templated carbon (GMgOC) or poly-GMA-unmodified MgO-templated carbon (NMgOC). The enzymes used were flavin adenine dinucleotide-dependent glucose dehydrogenase and bilirubin oxidase, with Azure-A serving as the mediator. Admittance analysis was utilized to measure enzyme activity and estimate the charge transfer resistance by extrapolating the spectra obtained through admittance analysis. The charge transfer resistances of both electrodes exhibited greater stability for the GMgOC electrode. This can be attributed to the covalent immobilization of the enzyme and mediator on the electrode facilitated by GMgOC, effectively suppressing enzyme and mediator elution. The electric double-layer capacitance values of both electrodes indicated the overall stability of the electrode structure during the measurement.