Mango (Mangifera indica) and peach (Prunus persica) juices are highly perishable, requiring innovative preservation methods to enhance their nutritional value and shelf life. This study evaluates the effect of single-cell protein (SCP) derived from Saccharomyces cerevisiae on the composition and stability of these juices. SCP fortification significantly increased protein content (mango: 0.47% to 0.91%, peach: 0.42% to 0.85%) and fiber (mango: 0.31% to 0.75%, peach: 0.30% to 0.71%), while reducing fat content. Antioxidant capacity improved, with flavonoid content rising (mango: 36.57 to 52.78 mg QE/mL, peach: 34.25 to 48.91 mg QE/mL) and DPPH activity increasing (mango: 39.52% to 62.37%, peach: 37.46% to 59.28%). Ascorbic acid levels, mineral content (calcium, magnesium), and superoxide dismutase activity also showed notable enhancements. SCP treatment slightly increased pH and viscosity, contributing to juice stability. Sensory evaluation confirmed improved color, aroma, and taste, enhancing consumer acceptability. These findings highlight SCP as a sustainable, functional additive for improving the nutritional quality and shelf life of fruit juices, offering potential applications in the food industry.