The agri-food processing industry predominantly relies on fossil fuels, contributing significantly to greenhouse gas emissions and extensive water use. Climate change requires a conversion of food processing technologies towards sustainability. Our research focuses on testing and validating pulsed electric field (PEF) technology as a mild processing method for stabilizing freshly squeezed, not from concentrate, blood orange juice. Experiments were carried out on a continuous pilot plant endowed with a patented treatment chamber that ensures a constant flow of product without “hot spots” for a homogeneous treatment. Once the operative conditions of the process in terms of energy density were optimized, PEF-treated blood orange juice was tested in order to evaluate the effects on physico-chemical parameters (total soluble solids, total acidity, pH, CIE L*, a*, b*, C*, h color indices, cloud, bioactive compounds (ascorbic acid, total anthocyanins, total and individual flavanones), antioxidant activity (ORAC units, total phenolic content), microbial communities (aerobic mesophilic viable count, yeasts and molds, acid-tolerant microorganisms), residual enzymatic pectinmethylesterase activity, and sensory attributes (flavor, off-flavor, off-odor, color, intensity of odor, acidity, sweetness, bitter, freshness, cooked flavor). Then, in order to simulate the commercial refrigerated distribution of PEF-treated blood orange juice and define its refrigerated shelf-life, the PEF-treated freshly squeezed, not from concentrate, blood orange juice was subjected to physico-chemical, antioxidant, microbiological, and sensory evaluations over twenty days of refrigerated storage at 4 ± 1 °C. The PEF treatment effectively ensured excellent microbial inactivation and enhanced the nutritional and health characteristics of the juice, thereby extending its shelf-life. This study demonstrates the significant potential of the PEF treatment to produce blood orange juice suitable for a new retail segment—freshly squeezed juices with superior health quality, fresh-like characteristics, and extended refrigerated shelf-life.