The novel biological denitrification process with electrochemical system using the bio-cathode of microbial fuel cells (MFC) presents a promising approach to reduce electron donor consumption during wastewater treatment. This method of autotrophic denitrification can utilize inorganic compounds (such as H2, S2-, S2O32- etc.) or electrodes (at a constant potential) to provide electrons for the denitrification process. This study focuses on an isolated autotrophic denitrifier strain Lyy (belonging to Stutzerimonas) and its application in bio-cathode denitrification. It was found that the extracellular electron transfer (EET) pathway between strain Lyy and electrode is facilitated via the electron shuttle phenazine-1-carboxylic acid (PCA). Especially, at a potential of −0.6 V (vs. SCE), strain Lyy can mediate inward EET from electrodes or inorganic compound into cells, enhancing denitrification with a NO3--N removal efficiency of 98.68 ± 0.68 % within 48 h. On the other hand, effective denitrification was achieved by the bio-cathode MFC without organic carbon sources. Meanwhile, the MFC exhibited a maximum output voltage of 172 ± 6 mV and a maximum power density of 77.46 ± 6.49 mW m−2 at a load resistance of 1 kΩ, with a NO3--N removal efficiency higher than 95 % and with no detecteable NO2--N, which implied that bio-cathode denitrification contributes to the electricity generation. This study showed bidirectional EET phenomena and expands the potential applications for treating low-carbon, high-nitrogen wastewater using strain Lyy.