Here, fundamental aspects affecting template-assisted engineering of oxidase-associated peroxide oxidation co-catalysis of the modeled microanalytical system based on the hybrid palladium nanoparticles (Pd-NPs) with tailored functional properties were studied. By an accurate tuning and validation of the experimental setup, a modular Pd-NPs-doped one-pot/one-electrode amperometric nanobiosensor for advanced multiplex analyte detection was constructed. The specific operational conditions (electrochemical read-out mode, pH, regeneration procedure) of the modular one-pot/one-electrode nanobiosensor allowed a reliable sensing of L-lactate (with linear dynamic range, LDR=500 µM – 2 mM, R2 =0.977), D-glucose (with LDR=200 µM – 50 mM, R2 =0.987), hydrogen peroxide (with LDR=20 µM – 100 mM, R2 =0.998) and glutaraldehyde (with LDR=1 – 100 mM, R2 =0.971). In addition, mechanistic aspects influencing the performance of Pd-NPs-doped one-pot/one-electrode for multiplex analyte sensing were studied in detail. The designed one-pot/one-electrode amperometric nanobiosensor showed a thin layer electrochemical behavior that greatly enhanced electron transfer between the functional hybrid layer and the electrode. Finally, a specific regeneration procedure of the hybrid one-pot/one-electrode and algorithm towards its usage for modular biocatalysis were developed. The reported strategy can readily be considered as a guideline towards the fabrication of commercialized nanobiosensors with tailored properties for advanced modular biocatalysis.