This study tests the hypothesis that altering the mineral composition of soil influences microbial community structure in a nutrient-deficient soil. Microcosms were established by adding mica (M), basalt (B) and rock phosphate (P) to soil separately, and in combination (MBP), and by planting with Lolium rigidum, Trifolium subterraneum or by leaving unplanted. The effects of mineral and plant treatments on microbial community structure were assessed using automated ribosomal intergenic spacer analysis. Bacterial community structure was significantly affected by both mineral (global R=0.73 and P < 0.001) and plant (global R=0.71 and P < 0.001) treatments, as was the fungal community structure: mineral (global R=0.65 and P < 0.001) and plant (global R=0.65 and P < 0.001) treatments. All pairwise comparisons of bacterial and fungal communities between different mineral treatments and between different plant treatments were significantly different (P < 0.05). This study has shown that mineral addition to soil microcosms resulted in substantial changes in both bacterial and fungal community structure, dependent on the type of mineral added and the plant species present. These results suggest that the mineral composition of soil may be an important factor influencing the microbial community structure in soil.