The super high-density (SHD) production system has recently been introduced to the Chilean European plum (Prunus domestica L.) industry, but the potential of applying regulated deficit irrigation (RDI) in this system remains unexplored. As irrigation water availability in Chile has been strongly jeopardized by climate change, there is an urgent need to validate water-conserving practices in modern production systems. A field study was conducted in a commercial SHD European plum orchard (cv. French grafted on Rootpac-20 rootstock) for two consecutive seasons in Peralillo, O'Higgins Region, Chile. The objective of this study was to assess the impact of a late water deficit (LD) on water productivity, fruit quality, plant water relations, and soil microbiota. The results showed that implementing LD enhanced water productivity by 40% without compromising fresh and dry fruit quality. Moderate to severe water stress induced no changes in physiological parameters such as stomatal conductance and photochemical efficiency. Additionally, the LD treatment significantly reduced soil moisture but increased the abundance of certain groups of beneficial soil microbiota and fine roots. These results highlight the potential of LD as a viable water-conserving practice in modern SHD European plum orchards, particularly in regions facing water scarcity due to climate change.