Pesticides pose a serious risk to ecosystems. In this study, we used European Food Safety Authority methods, such as risk quotient (RQ) and toxicity exposure ratios (TER), to assess the potential ecological risks of 15 pesticide residues detected in agricultural soils in the Gaidahawa Rural Municipality of Nepal. The mean and maximum concentrations of the detected pesticide residues in the soil were used for risk characterization related to soil organisms. RQmean, TERmean and RQmaximum, TERmaximum were used to determine general and the worst-case scenarios, respectively. Of all the detected pesticides in soils, the no observed effect concentration (NOEC) for 27% of the pesticides was not available in literature for the tested soil organisms and their TER and RQ could not be calculated. RQ threshold value of ≥1 indicates high risk for organisms. Similarly, TER threshold value of ≥5, which is acceptable trigger point value for chronic exposure, indicates an acceptable risk. The results showed that the worst-case scenario (RQmaximum) indicated a high risk for soil organisms from chlorpyrifos [RQmaximum > 9 at depths (cm) of 0–5, 15–20 and 35–40 soil layer]; imidacloprid (1.78 in the 35–40 cm soil layer) and profenofos (3.37 in the 0–5 cm and 1.09 in the 35–40 cm soil layer). Likewise, for all the soil depths, the calculated TER for both the general and worst-case scenarios for chlorpyrifos ranged from 0.37 to 3.22, indicating chronic toxicity to F. candida. Furthermore, the risk of organophosphate pesticides for soil organisms in the sampling sites was mainly due to chlorpyrifos, except for two study sites where the risk was from profenofos. Ecological risk assessment (EcoRA) of the pesticide use in the study area indicated that the EFSA soil organisms were at risk at some of the localities where farmers practiced conventional farming.