The use of pesticides in crop fields may have negative effects on soil Oligochaeta Annelida, i.e., earthworms and enchytraeids, and thus affect soil quality. The aim of this study was to assess the effects of two commercial fungicide formulations on the earthworm Aporrectodea caliginosa and the enchytraeid Enchytraeus albidus in a natural soil. The fungicides were Cuprafor micro® (copper oxychloride), commonly used in organic farming, and Swing Gold® (epoxiconazole and dimoxystrobin), a synthetic fungicide widely used in conventional farming to protect cereal crops. Laboratory experiments were used to assess the survival, biomass loss and avoidance behaviour. No lethal effect was observed following exposure to the copper fungicide for 14 days, even at 5000 mg kg−1 of copper, i.e. 650 times the recommended dose (RD). However, a significant decrease in biomass was observed from 50 mg kg−1 of copper (6.5 times the RD) for A. caliginosa and at 5000 mg kg−1 of copper (650 times the RD) for E. albidus. These sublethal effects suggest that a longer period of exposure would probably have led to lethal effects. The EC50 avoidance for the copper fungicide was estimated to be 51.2 mg kg−1 of copper (6.7 times the RD) for A. caliginosa, and 393 mg kg−1 of copper (51 times the RD) for E. albidus. For the Swing Gold® fungicide, the estimated LC50 was 7.0 10−3 mL kg−1 (6.3 times the RD) for A. caliginosa and 12.7 10−3 mL kg−1 (11.0 times the RD) for E. albidus. No effect on biomass or avoidance was observed at sublethal concentrations of this synthetic fungicide. It was concluded that enchytraeids were less sensitive than earthworms to the two commercial fungicides in terms of mortality, biomass loss and avoidance behaviour. Therefore we discuss the different strategies possibly used by the two Oligochaeta species to cope with the presence of the pesticides were discussed, along with the potential consequences on the soil functions.