•PRD was found to be a valuable and sustainable production strategy.•PRD induced physiological mechanisms responses enabling trees to tolerate the imposed water stress.•Monitoring transpiration by heat pulse sap flow measurements is an effective tool for detection of drought stress.•ERT monitoring allows to identify the root water uptake processes at fine spatial scale. We have studied the effects of partial root-zone drying (PRD) on plant physiological response, plant-soil water dynamics, yield and fruit quality of young orange trees during the irrigation seasons 2013 and 2014 in an orchard located in Eastern Sicily (Southern Italy). The irrigation treatments included: (i) full irrigation (T1), with trees irrigated by supplying 100% of crop water demand using micro-irrigation systems; and (ii) alternate partial root-zone drying (T4), with trees irrigated at 50% of crop water demand. Minimally invasive electrical resistivity tomography (ERT) was adopted to help quantify root-water-uptake (RWU) processes at the finer (decimetric) spatial scale. Results show that, compared with the full irrigation treatment, PRD at 50% of crop water demand (ETc) increased the fruit yield by 20% in 2013 and 10% in 2014. The PRD irrigation treatment, which induces a reduction of the wetted soil volumes, had also obvious positive effects on water use efficiency (WUE), compared to full irrigation. From the results of this study, we concluded that when water resources are limited, PRD at 50% level of ETc is an efficient water saving strategy to increase WUE, while other physiological and growth parameters are practically unaffected.