Phosphonate foliar applications in the period before harvest are routinely used in citrus (Citrus sp.) production for the control of phytophthora brown rot (Phytophthora sp.) control. However, several grower reports indicated that these applications caused phytotoxic damage on ‘Nadorcott’ mandarin (Citrus reticulata hybrid) fruit. To investigate this, trials were conducted over two seasons (2016 and 2017) in two climatically different citrus production areas of South Africa. These trials consisted of ammonium and potassium phosphite foliar applications (at full dose or half dose) at green, color break, or full color stages of fruit development. At commercial harvest, fruit was sampled from the different treatments and the incidence of the phytotoxic damage was documented as both percentage incidence and a phytotoxic index (PI). Results indicated that, regardless of the type of phosphonate or dosage applied, phytotoxic damage was observed at harvest if foliar applications were carried out at color break or full color stage of fruit development. The same results were observed in the different climatic areas, although the mean percentage of damaged fruit varied between the areas. Based on these results it is recommended that skirt pruning be used to mitigate phytophthora brown rot on ‘Nadorcott’ mandarin fruit.