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Microbial processes are crucial in the redox transformations of toxic selenium oxyanions. This study focused on isolating an efficient selenate-reducing strain, Azospira sp. A9D-23B, and evaluating its capability to recover extracellular selenium nanoparticles (SeNPs) from selenium-laden wastewater in different reactor setups. Analysis using transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDX) revealed significantly higher extracellular SeNPs production (99%) on the biocathode of the bioelectrochemical (BEC) reactor compared to the conventional bioreactor (65%). Further investigations into the selenate reductase activity of strain A9D-23B revealed distinct mechanisms of selenate reduction in BEC and conventional bioreactor settings. Notably, selenate reductases associated with the outer membrane and periplasm displayed higher activity (18.31 ± 3.8 µmol/mg-min) on the BEC reactor's biocathode compared to the upflow anaerobic conventional bioreactor (3.24 ± 2.9 µmol/mg-min). Conversely, the selenate reductases associated with the inner membrane and cytoplasm exhibited lower activity (5.82 ± 2.2 µmol/mg-min) on the BEC reactor's biocathode compared to the conventional bioreactor (9.18 ± 1.6 µmol/mg-min). However, the comparable kinetic parameter (K_m) across cellular fractions in both reactors suggest that SeNPs localization was influenced by enzyme activity rather than selenate affinity. Overall, the mechanism involved in selenate reduction to SeNPs and the strain's efficiency in detoxifying selenate below levels regulated by U.S. Environmental Protection Agency have broad implications for sustainable environmental remediation strategies.