The increasing popularity of seed treatment applications in agriculture may leave unintended hazards to soil biota, such as earthworms. The objective of this study was to explore mitochondrial DNA toxicity resulting from sublethal exposures to systemic pesticides, including four neonicotinoid insecticides (neonics), as well as coexposure to difenoconazole (DIF), a triazole fungicide, in earthworms (Eisenia fetida) in vivo. Earthworms were exposed under dose regimes resembling label recommendation and levels left in soil post seed treatment application for 30 days in an earthworm breeding facility. Mitochondrial DNA copy numbers (mtDNAcn) in earthworms were determined by using the 2 −ΔCt algorithm. Earthworms' body weights were recorded before and after the exposure period. We found a highly significant increase of mtDNAcn in earthworms across all exposure groups (ANOVA, p < 0.001), either under a single neonic or combined with DIF exposure. Coupled with mtDNA toxicity, earthworms in the treatment groups gained significantly less weight than control earthworms (ANOVA, p < 0.001). We concluded that systemic pesticides, both neonics and DIF, posed mtDNA toxicity as measured by mtDNAcn, in earthworms.