Surface defects have been shown to facilitate electron transfer between Fe(II) and goethite (α-FeOOH) in abiotic systems. It is unclear, however, whether defects also facilitate microbial goethite reduction in anoxic environments where electron transfer between cells and Fe(III) minerals is the limiting factor. Here, we used stable Fe isotopes to differentiate microbial reduction of goethite synthesized by hydrolysis from reduction of goethite that was further hydrothermally treated to remove surface defects. The goethites were reduced by Geobacter sulfurreducens in the presence of an external electron shuttle, and we used ICP-MS to distinguish Fe(II) produced from the reduction of the two types of goethite. When reduced separately, goethite with more defects has an initial rate of Fe(III) reduction about 2-fold higher than goethite containing fewer defects. However, when reduced together, the initial rate of reduction is 6-fold higher for goethite with more defects. Our results suggest that there is a suppression of the reduction of goethite with fewer defects in favor of the reduction of minerals with more defects. In the environment, minerals are likely to contain defects and our data demonstrates that even small changes at the surface of iron minerals may change their bioavailability and determine which minerals will be reduced.