Large quantities of strobilurin fungicides (SFs) are used worldwide, resulting in adverse effects on non-target organisms. SFs affect the reproduction and embryonic development of aquatic organisms, while the impact on soil organisms has been insufficiently researched. Therefore, we investigated the effects of three SFs (azoxystrobin (AZO), pyraclostrobin (PYR), and trifloxystrobin (TRI)) on the survival, reproduction, and hatching success of the non-target soil oligochaete Enchytraeus crypticus. The standard enchytraeid reproduction test (ERT) showed that, regarding survival, TRI (LC50 = 2.34 mg/kg) was the most toxic, followed by PYR (LC50 = 4.26 mg/kg) and AZO (LC50 ≥150 mg/kg). Reproduction was affected in the same order (TRI EC50 = 0.045 mg/kg, PYR EC50 = 1.85 mg/kg, and AZO EC50 = 93.10 mg/kg). Exposure to AZO and PYR showed a negative impact on hatching success with a significant increase in the number of unhatched cocoons. Prolonged hatching test was consequently carried out. As a result, a hatching delay was observed at lower AZO and PYR concentrations, while at higher concentrations hatching was completely stopped as the cocoons were no longer viable. Hence, hatching test enabled a discrimination between hatching delay and hatching impairment. Besides demonstrating the adverse effects of AZO, PYR, and TRI on the survival, reproduction, and hatching success of E. crypticus, the obtained results indicate the convenience of using several endpoints in reproduction tests. The usage of prolonged hatching tests and monitoring of hatching dynamics could fill the gap between standard reproduction tests and multigeneration tests and allow a better understanding of the adverse effects on reproduction.