Microplastics negatively impact soil health and productivity. Organic fertilizers constitute significant contributors of microplastics in agricultural soils. Nevertheless, comprehensive data on the diversity of microplastics in long-term fertilized soils remain unavailable. In this study, we assessed the presence of microplastics in soils subjected to application of three different organic fertilizers (pig manure, chicken manure, and sludge composts) over 12 years, and evaluated the potential ecological risks posed by microplastic accumulation. The average microplastic abundance in soil was 368.88 ± 207.97 (range: 90–910) items/kg. Microplastic abundance differed among fertilization treatments, with substantial increases of 16.67%, 71.67%, and 61.43% upon low to high application of the three treatments, respectively. Overall, the microplastics predominantly comprised fibers (70.94%) and fragments (25.25%), of which a substantial proportion constituted light-colored microplastics (transparent and white). The size of microplastics was mainly concentrated in the 1–2 mm range (39.96%), with rayon, polypropylene, polyester, and polyethylene being identified as the major types. The risk assessment indices of the three treatments were 229.38, 257.64, and 175.89, respectively, and were all classified as level 4 (high risk). The microplastic diversity integrated index and principal component analysis revealed that microplastics were uniformly distributed throughout the 0–20 cm soil depth consequent to tillage activity. Together, these findings provide a comprehensive assessment of microplastic pollution in long-term fertilized soils and serve as a scientific basis for reducing microplastic contamination in agricultural soils.