Microbial species interactions are expected to influence the community-level properties, such as the production of extracellular enzymes and the degradation of organic substances. This work examined how microbial diversity, composition and the overall sign of microbial associations were altered with soil texture and structure following the amendment of organic substances. Two sets of microcosms (1:100 and 1:1) of a 4 × 3 factorial design were constructed, with four artificial textural classes (a sandy loam, two loams, and a (silty) clay loam) and three organics (TSB, tryptic soy broth; CA, a mixture of cellulose and humic/fulvic acids; BS, barley straw). As the ‘microbial inoculant’, an agricultural soil was added to the 1:100 and 1:1 microcosms at 1% and 50%, respectively. A few of microbial taxa were specifically enriched after soil addition of TSB, CA, or BS, but distributions across textural classes were inconsistent between microcosms or between organic amendments. Regardless, top abundant bacterial and fungal OTUs were overall negatively associated, suggesting that microbial competition for the shared resource dominated the decomposition of both simple and complex organics. Microbial associations were also modified by soil pore size distribution (PSD), being fewer negative (or more positive) in soils of greater macroporosity than in soils of lower macroporosity. The PSD-based differences in microbial associations were coordinated with PSD-based differences in the activities of exoglucanase and β-glucosidase in TSB-amended soils or soil respiration characteristics in CA-amended soils. Our results provide new insight into how soil structure regulates microbial interactions and, accordingly, the degradation of organic matter.