The use of zinc oxide nanoparticles (ZnO NPs), applied as a possible micronutrient source, in conjunction with organic pesticides in agricultural soils has the potential to alter the environmental behavior and toxicity of these chemicals to soil biota. This research examines the joint effects of ZnO NPs and the herbicide metribuzin (MTZ) on phytotoxicity to plants, toxicity to soil microorganisms, and the accumulation of Zn and MTZ in plants. After 23 days, effects on growth, photosynthetic pigment content, and oxidative stress biomarkers in bean plants (Phaseolus vulgaris) and soil enzymatic activities were evaluated. Additionally, the amounts of Zn and MTZ (and the latter’s main metabolites) in soil and plant tissues were quantified. ZnO NPs reduced ammonium oxidase activity and growth among MTZ-stressed plants while reducing photosynthetic pigment levels and enhancing antioxidant enzymatic activities. MTZ had a marginal impact on the availability and accumulation of Zn in plant tissues, although significant effects were observed in some specific cases. In turn, ZnO NPs drastically affected MTZ degradation in soil and influenced MTZ accumulation/metabolization in the bean plants. Our findings indicate that the indirect effects of ZnO NPs, through their interaction with commonly used organic pesticides, may be relevant and should be taken into account in agricultural soils.