Understanding the redox transformations of selenium (Se) under varying redox atmospheres is critical for predicting its environmental fate and optimizing Se removal from contaminated wastewater. However, the influence of redox atmospheres, specifically H2 and O2, on Se transformation mechanisms and the structural nature of the resulting Se(0) remains poorly understood. In this study, we investigated the interactions between aqueous selenate (Se(VI)) and Fe(II)-bearing minerals (pyrite, magnetite and mackinawite) under N2, H2 and air atmospheres, employing comprehensive characterizations on both aqueous and solid speciation. Our findings reveal that H2 and air atmospheres could enhance Se removal by pyrite but limit its removal by mackinawite, while magnetite shows no significant atmospheric influence on Se removal. Alongside Se removal, sorbed Se(VI) was transformed into distinct elemental Se depending on the mineral: trigonal γ-Se nanoneedles on magnetite, monoclinic β-Se on mackinawite, and nanosized amorphous Se(0) on pyrite. Moreover, H2 significantly lowered the solution redox potential, favoring the reduction of sorbed Se(VI) to Se(0) or FeSex. Overall, this work provides valuable insights for optimizing Se remediation and recovery strategies in Se-contaminated wastewater and improving understanding of Se behavior in diverse geochemical systems, including nuclear waste disposal repositories.