Microbial products, largely the necromass, are key contributors to stable soil organic matter (SOM) in terrestrial systems, and microbial communities may differ in the stabilization. Plants can control microbial communities through litter quality and entry sites of plant inputs (above- or below-ground). However, whether soil mineral fractions (due to the characteristics such as soil texture) can also control the microbial communities, remains unclear. We conducted two model soil incubation experiments (E1 and E2) in order to simulate the four field soils. Materials included were plant materials, such as general plant inputs in soil systems, and four mineral materials derived from different field soils (i.e., “the four original field soils”), with their SOM removed by combustion. E1 was undertaken to simulate root exudate using oxalate and glucose, and E2 was undertaken to simulate plant litter using broad leaves, coniferous leaves, branches, and fine roots. The microbial (mainly bacterial) community structure from phospholipid fatty acid (PLFA) across E1 and E2 showed differences due to the mineral materials, and the differences after accounting for plant materials are similar to the difference in the four original field soils. Additionally, the abundance of bacterial PLFAs in E2 increased with silt and clay content and was correlated with the abundance of the bacterial PLFAs in the four original field soil. This study implies that even in the case of this experiment under such conditions as a broad variety of plant inputs, mineral fractions strongly influence bacterial communities, in a manner consistent with field soil systems.