Microbial electrosynthesis is a promising alternative to directly convert CO₂ into long-chain compounds by coupling inorganic electrocatalysis with biosynthetic systems. However, problems arose that the conventional electrocatalysts for hydrogen evolution may produce extensive by-products of reactive oxygen species and cause severe metal leaching, both of which induce strong toxicity toward microorganisms. Moreover, poor stability of electrocatalysts cannot be qualified for long-term operation. These problems may result in poor biocompatibility between electrocatalysts and microorganisms. To solve the bottleneck problem, Co anchored on porphyrinic triazine-based frameworks was synthesized as the electrocatalyst for hydrogen evolution and further coupled with Cupriavidus necator H16. It showed high selectivity for a four-electron pathway of oxygen reduction reaction and low production of reactive oxygen species, owing to the synergistic effect of Co–N_x modulating the charge distribution and adsorption energy of intermediates. Additionally, low metal leaching and excellent stability were observed, which may be attributed to low content of Co and the stabilizing effect of metalloporphyrins. Hence, the electrocatalyst exhibited excellent biocompatibility. Finally, the microbial electrosynthesis system equipped with the electrocatalyst successfully converted CO₂ to poly-β-hydroxybutyrate. This work drew up a novel strategy for enhancing the biocompatibility of electrocatalysts in microbial electrosynthesis system.