Soil microplastic contamination is emerging as a significant environmental concern affecting soil properties and biota, including soil aggregation. This study aimed to determine the influence of soil microplastics on soil aggregation, their impact through effects on soil microorganisms, and their effects on water and mechanical stability of soil aggregates. Soil incubation experiments were conducted using sterilized and non-sterilized soils with 15-μm polyethylene and polylactic microplastics over one month. Sterilized soils showed more water-stable aggregates, particularly in the 0.25–0.5 mm fraction (+49%), with both polyethylene and polylactic MPs significantly increasing this fraction (+34% and +35%, respectively). However, no significant effects of soil sterilization and MP addition were found on mechanical stability. The addition of MPs tended to decrease aggregate surface roughness but not significantly (−17~21%). The study provides insights into the complex interactions between microplastics and soil aggregation, suggesting that MP effects may not necessarily be related to their toxicity on soil microbes but could involve various physical interactions.