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Boron (B) affects plasma membrane (PM) integrity and consequently modulates the P‐type PM H+‐ATPase activity creating a driving force for nutrient influx at the root level. Because citrus rootstocks respond differently to B supply, we hypothesised that PM H+‐ATPase activity of varieties contrasting in horticultural traits would affect nutrient uptake by trees. Sweet orange (Citrus sinensis) trees grafted onto Rangpur lime (RL; Citrus limonia) or Swingle citrumelo (SW; Citrus paradisi × Poncirus trifoliata) were grown in nutrition solution with four B concentrations (0 [control concentration], 46, 230 and 460 μM B, as H3BO3) up to 7 days of treatment imposition after plant adaptation into the hydroponic condition. SW exhibited higher B absorption, leaf B and enzyme activity than RL. The highest enzyme activity was achieved with 230 μM of B 1 day after treatment imposition (ATI), whereas B excess impaired the PM H+‐ATPase in all periods evaluated. Absorption of mineral nutrients correlated with PM H+‐ATPase activity, with greater nutrient uptake per root unit in SW compared to RL. Leaf and root nutrient concentrations were equivalent to amounts absorbed and enzyme activity, with greater increments exhibited by trees grafted onto SW compared to RL. Effects of B supply on PM H+‐ATPase activity explain distinct nutrient uptake patterns by trees, what supports fine‐tuning fertilisation guidelines of citrus taking into account rootstock varieties.