•A single foliar spray with relatively low amounts of B or Zn nano-fertilizers (34mgBtree−1 or 636mgZntree−1, respectively) led to increases in pomegranate fruit yield.•Fertilization with the highest of the two doses led to significant improvements in fruit quality, including TSS, decreases in TA, and increases in maturity index and pH in juice.•Physical fruit characteristics were unaffected. Changes in total sugars and total phenolic compounds were only minor, whereas the antioxidant activity and total anthocyanin were unaffected. This study was carried out to assess the effects of the foliar application of nano-fertilizers of zinc (Zn) and boron (B) on pomegranate (Punica granatum cv. Ardestani) fruit yield and quality. A factorial experiment was conducted based on a completely randomized block design, with nine treatments and four replications per treatment. Foliar sprays of nano-Zn chelate fertiliser at three concentrations (0, 60 and 120mgZnL−1) and nano-B chelate fertiliser (0, 3.25 and 6.5mgBL−1) were applied as a single spray before full bloom at a rate of 5.3Ltree−1. The application of Zn and B increased the leaf concentrations of both microelements in August, reflecting the improvements in tree nutrient status. A single foliar spray with relatively low amounts of B or Zn nano-fertilizers (34mgBtree−1 or 636mgZntree−1, respectively) led to increases in pomegranate fruit yield, and this was mainly due to increases in the number of fruits per tree. The effect was not as large with Zn as with B. Fertilization with the highest of the two doses led to significant improvements in fruit quality, including 4.4–7.6% increases in TSS, 9.5–29.1% decreases in TA, 20.6–46.1% increases in maturity index and 0.28–0.62pH unit increases in juice pH, whereas physical fruit characteristics were unaffected. Changes in total sugars and total phenolic compounds were only minor, whereas the antioxidant activity and total anthocyanins were unaffected.