Zinc and boron are nutrients that often suffer low bioavailability to pecan trees grown in calcareous soils whereas adequate supplies of these two elements is essential for commercial pecan production. Working with young pecan trees, we evaluated changes in oxidative metabolism, levels of bioactive compounds, yield components and foliar nutrient concentrations in response to foliar sprays (50 or 100 mg L−1) of zinc oxide nanoparticles (ZnO NPs) and boron (H3BO3). Four different treatment solutions were applied in a completely randomised design with six replications per treatment (24 trees in total). Zinc and B treatments were applied before pistil receptivity (3 weeks before anthesis) and at stem elongation stage 31, 39/60; flowering stage 69; fruit stages 7–75 and continued for a total of five applications at 14-day intervals. We evaluated enzyme activities (SOD, H2O2, CAT and GPx), AC, phenols, flavonoids, leaf area, chlorophyll, total anthocyanins and nut yield and quality (nut weight and % kernel). The mineral concentrations in the leaflets were also determined. The mineral concentrations (N, P, K, Ca, Mg, Fe, Cu, Mn, Ni, Zn and B) in the leaflets were also determined. Spraying ZnO NPs and B increased SOD activity, CA, chlorophyll concentration, mineral nutrients (N, K, Ca, Zn and B) and yield. However, reductions were observed for CAT activity, nut quality and concentrations of phenol, flavonoid, anthocyanin and Fe. Boron increased GPx activity and P concentration. These results demonstrate that spraying low doses (50 mg L−1) of ZnO NPs and B can help reduce oxidative stress and increase yield, nut quality and leaf concentrations of Zn and B in young cv. Wichita pecan trees established on a calcareous soil.