In this study, the biotite weathering activities of strain S41 and mutants with deletion of the iron response regulator genes fur, rirA, and irr were compared. S41ΔrirA had a 35%–60% increase in Fe and Al concentrations, a 95%–112% increase in siderophore production, and a 18%–22% increase in EPS concentration, while S41Δirr had a 29%–48% decrease in Fe and Al concentrations and a 32%–42% decrease in siderophore production, compared with strain S41. Under iron-sufficient conditions, S41ΔrirA had a 1.5-fold–2.7-fold increase in siderophore production, while there was similar siderophore production between strain S41 and S41Δirr. Under iron-limited conditions, S41Δirr had a 34%–40% decrease in siderophore production compared with strain S41. The expression of genes related to the synthesis of siderophores, iron uptake and transporters, and EPS production in strain S41 significantly increased in iron-limited conditions compared with that in iron-sufficient conditions. The expression of genes associated with the synthesis of siderophores and iron uptake and transporters significantly increased in S41ΔrirA in iron-sufficient and iron-limited conditions but decreased in S41Δirr in iron-limited conditions. Our results suggested that rirA- and irr-modulated multiple genes may be related to the mineral weathering activities of strain S41.