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This study investigated the effect of different processing conditions on the properties of emulsions and final microcapsules in a pilot scale. A mixed protein system of sodium caseinate and pea protein isolate was used as wall material. The potential correlations amongst properties of emulsions and spray-dried powders, and the stability of nutrients were studied using coefficient correlation analysis. Increasing homogenization pressure or number of passes increased the retention of β-carotene significantly, while increasing the inlet air temperature was effective in preserving Vitamin A. Two-pass homogenization helped to achieve a smaller droplet size of liquid emulsions, which resulted in lower free-fat, higher nutrient retention, and better oxidative stability of powdered microcapsules. Increasing the inlet air temperature led to a higher tendency of lipid oxidation of spray-dried powders. A lower inlet temperature at 127°C increased the water activity and decreased the glass transition temperature of spray-dried powders, which consequently resulted in powder caking.