Although microplastics (MPs) are ubiquitous in agricultural soil, little is known about the effects of MPs combined with pesticides on soil organisms and their biogenic transport through the soil profile. In this study, we conducted mesocosm experiments to observe the effects of microplastics (polyethylene (LDPE-MPs) and biodegradable microplastics (Bio-MPs)) and chlorpyrifos (CPF) on earthworm (Lumbricus terrestris) mortality, growth and reproduction, as well as the biogenic transport of these contaminants through earthworm burrows. The results showed that earthworm reproduction was not affected by any treatment, but earthworm weight was reduced by 17.6% and the mortality increased by 62.5% in treatments with 28% Bio-MPs. Treatments with 28% LDPE-MPs and 7% Bio-MPs combined with CPF showed greater toxicity while the treatment with 28% Bio-MPs combined with CPF showed less toxicity on earthworm growth as compared to treatments with only MPs. The treatments with 1250 g ha−1 CPF and 28% Bio-MPs significantly decreased the bioaccumulation of CPF in earthworm bodies (1.1 ± 0.2%, w w−1), compared to the treatment with CPF alone (1.7 ± 0.4%). With CPF addition, more LDPE-MPs (8%) were transported into earthworm burrows and the distribution rate of LDPE-MPs in deeper soil was increased. No effect was observed on the transport of Bio-MPs. More CPF was transported into soil in the treatments with LDPE-MPs and Bio-MPs, 5% and 10% of added CPF, respectively. In addition, a lower level of the CPF metabolite 3,5,6-trichloropyridinol was detected in soil samples from the treatments with MPs additions than without MP additions, indicating that the presence of MPs inhibited CPF degradation. In conclusion, Bio-MPs caused significant toxicity effects on earthworms and the different types of MPs combined with CPF affected earthworms differently, and their transport along the soil profile. Thus, further research is urgently needed to understand the environmental risks of MPs and MP-associated compounds in the soil ecosystem.