Nanoencapsulation of native potato bioactive compounds by spray-drying improves their stability and bioavailability. The joint effect of the inlet temperature and the ratio of the encapsulant (quinoa starch/gum arabic) on the properties of the nanocapsules is unknown. The purpose of this study was to determine the best conditions for the nanoencapsulation of these compounds. The effects of two inlet temperatures (96 and 116 °C) and two ratios of the encapsulant (15 and 25% w/v) were evaluated using a factorial design during the spray-drying of native potato phenolic extracts. During the study, measurements of phenolic compounds, flavonoids, anthocyanins, antioxidant capacity, and various physical and structural properties were carried out. Higher inlet temperatures increased bioactive compounds and antioxidant capacity. However, a higher concentration of the encapsulant caused the dilution of polyphenols and anthocyanins. Instrumental analyses confirmed the effective encapsulation of the nuclei in the wall materials. Both factors, inlet temperature, and the encapsulant ratio, reduced the nanocapsules’ humidity and water activity. Finally, the ideal conditions for the nanoencapsulation of native potato bioactive compounds were determined to be an inlet temperature of 116 °C and an encapsulant ratio of 15% w/v. The nanocapsules obtained show potential for application in the food industry.