From the start of the 21st century, nanoecotoxicological research has been growing in fast steps due to the need to evaluate the safety of the increasing use of engineered nanomaterials. Boron (B) and vanadium (V) nanoparticles (NPs) generated by anthropogenic activities are subsequently released in the environment; therefore, organisms can be continuously exposed to these NPs for short or long periods. However, the short and long-term effects of BNPs and VNPs on soil organisms are unknown. This work aimed to recognize and describe their potential toxicological effects on the model species Enchytraeus crypticus, assessing survival and reproduction, through a longer-term exposure (56 days (d)—OECD test extension of 28 d), and avoidance behavior, through a short-term exposure (48 hours (h)). After 28 d, BNPs did not induce a significant effect on E. crypticus survival, whereas they decreased the organisms’ reproduction at 500 mg/kg. From 10 to 500 mg/kg, VNPs decreased the E. crypticus survival and/or reproduction. After 56 d, 100 to 500 mg/kg BNPs and 50 to 500 mg/kg VNPs, decreased the reproduction output of E. crypticus. The estimated Effect Concentrations (ECx) based on reproduction, for BNPs, were lower at 56 d compared with 28 d; for VNPs, an opposite pattern was found: ECx 28 d < ECx 56 d. BNPs did not induce an avoidance behavior, but organisms avoided the soil contaminated with 10 mg VNPs/kg. The tested NPs showed different E. crypticus apical effects at 28 d from the ones detected at 56 d, dependent on the type of NPs (B vs. V). In general, VNPs showed to be more toxic than BNPs. However, the effects of VNPs were alleviated during the time of exposure, contrarily to BNPs (which became more toxic with extended duration). The present study adds important information about NPs toxicity with ecological significance (at the population level). Including long-term effects, the obtained results contributes to the improvement of NPs risk assessment.