Agricultural microplastic pollution has become a growing concern. Unfortunately, the impacts of microplastics (MPs) on agricultural soil carbon and nitrogen dynamics have not been sufficiently reported. In an attempt to remedy this, we conducted a 105-day out-door mesocosm experiment in a soil-plant system using sandy soils amended with two types of MPs, low-density polyethylene (LDPE-MPs) and biodegradable (Bio-MPs), at concentrations of 0.0% (control), 0.5%, 1.0%, 1.5%, 2.0% and 2.5% (w/w, weight ratio of microplastics to air-dry soil). Soil organic matter (SOM), dissolved organic carbon (DOC), permanganate oxidizable carbon (POXC), available nitrogen (AN) of N-NH4+ and N-NO3−, and dissolved organic nitrogen (DON) were measured on day 46 (D46) and 105 (D105) of the experiment. SOM was also measured after microplastics were mixed into soils (D0). For LDPE-MPs treatments, SOM on D0, D46 and D105 showed no significant differences, while for Bio-MPs treatments, SOM significantly (p < 0.05) decreased from D0 to D46. Compared to the control, soil POXC was significantly (p = 0.001) lowered by 0.5%, 1.0% and 2.5% LDPE-MPs and ≥ 1.0% Bio-MPs on D105. LDPE-MPs showed no significant effects on soil DOC and nitrogen cycling. 2.0% and 2.5% Bio-MPs showed significantly higher (p < 0.001) DOC and DON (on D46 and D105) and ≥1.5% Bio-MPs showed significantly lower (p = 0.02) AN (on D46). Overall, Bio-MPs exerted stronger effects on the dynamics of soil carbon and nitrogen cycling. In conclusion, microplastics might pose serious threats to agroecosystems and further research is needed.