Substitution of aluminum under natural environmental conditions has been proven to inhibit the transformation of weakly crystalline iron (oxyhydr)-oxides towards well crystalline iron oxides, thereby enhancing their long-term stability. However, exploration on the role of aluminum substitution in bacteria-mediated iron oxides transformation is relatively lacking, especially in the anaerobic underground condition where iron (oxyhydr)-oxides are easy to reduced. In this study, we selected four different levels of substitution aluminum prevalent in iron oxides under natural conditions, which are 0mol%, 10mol%, 20mol%, and 30mol% (mol Al/mol (Al + Fe)) respectively. With the presence of Shewanella oneidensis MR-1, we conducted a 15-day anaerobic microcosm experiment in simulated groundwater conditions. The experiment data suggested that aluminum substitution result in a decrease in bio-reduction rate constants of ferrihydrite from 0.24 in 0mol% Al to 0.17 in 30mol% Al. Besides, when containing substituted aluminum, secondary minerals produced by biological reduction of ferrihydrite changed from magnetite to akaganeite. These results were attributed to the surface coverage of Al during the reduction process, which affects the contact between S. oneidensis MR-1 and the unexposed Fe(III), thus inhibiting the further reduction of ferrihydrite. Since iron (oxyhydr)-oxides exhibit a strong affinity on multiple kinds of pollutants, results in this study may contribute to predicting the migration and preservation of contaminants in groundwater systems.