Many tree crops experience sub-optimal yields and low fruit quality due to inadequate pollination, low fruit set, and poor crop nutrition. Boron (B) is a critical crop nutrient for fruit set because B levels affect pollen germination and pollen tube growth. However, the relationship between floral B concentration and fruit set is not well understood. The aim of this study was to determine the effect of B applications on the initial fruit set, yield, quality, and paternity of macadamia (Macadamia integrifolia). Cultivar ‘816’ trees received one of three treatments: (a) 0 g, (b) 15 g, or (c) 30 g B per tree prior to flowering. Boron application increased the B concentration of macadamia flowers. Application of 15 g B increased fruit set at 3 weeks after peak anthesis, but this higher initial fruit set was not translated into higher fruit set at 6 or 10 weeks after peak anthesis or higher yield. Boron application increased B concentrations in kernels but did not affect nut-in-shell (NIS) mass, kernel mass, kernel recovery, kernel oil concentration or incidence of whole kernels. Cultivar ‘816’ was highly outcrossing, with 97–98% cross-paternity among kernels from all treatments. Our results indicate that higher B concentration in macadamia flowers can be associated with an increased initial fruit set. However, high B levels did not affect yield, nut quality, or the proportion of self-pollinated fruit at maturity. The heavy dependence on outcrossing highlights the importance of inter-planting different cultivars and managing bee hives to sustain the productivity of macadamia orchards.