The root lesion nematode (Pratylenchus brachyurus) is a major constraint in soybean (Glycine max (L.) Merr.) production in Brazil’s Midwest, where it causes significant yield losses. Weed management is also challenging, often requiring repeated herbicide applications. This study was developed in order to evaluate the effects of herbicides on P. brachyurus populations in conventional and transgenic soybean cultivars. Two experiments were carried out under naturally infested field conditions and in a greenhouse using a randomized block design. Treatments included four weed control methods (manual weeding, lactofen, chlorimuron-ethyl, and haloxyfop) applied to two conventional cultivars (BRSGO Iara and M-Soy 8001), plus two additional treatments on the transgenic cultivar BRS Valiosa RR (manual weeding and glyphosate). In the field, nematode density and reproduction factor were assessed at 45 and 90 days after emergence, along with root mass, leaf area, and pod biomass. Chlorimuron-ethyl increased nematode populations in both conventional cultivars, while lactofen reduced them in M-Soy 8001. Haloxyfop lowered the reproduction factor, and both chlorimuron and lactofen negatively affected plant growth. In the greenhouse, evaluations at 30 and 60 days after inoculation included nematode density and root and shoot biomass. At 30 DAI, chlorimuron increased nematode density in M-Soy 8001, while lactofen reduced it; all herbicides reduced shoot biomass. At 60 DAI, only glyphosate reduced shoot biomass in the transgenic cultivar. Overall, specific herbicides affected both nematode dynamics and plant development, with responses varying by cultivar and environment.