Interactions of food proteins and lipids under oxidative conditions may lead to alterations in food texture as well as loss of nutritional and sensory quality. Oxidative and physical stability of oil-in-water emulsions stabilized with water-soluble proteins extracted from quinoa (Chenopodium quinoa) and amaranth (Amaranthus caudatus) was monitored in an oxidation study at 30 °C for 7 days. Alkaline extraction of proteins from the flours followed by acid precipitation and freeze-drying was conducted and purified rapeseed oil was used to prepare emulsions via high-pressure microfluidizer. Protein-stabilized emulsions showed lower physical and oxidative stability compared to Tween® 20-stabilized emulsions. Lipid oxidation volatile profiles of protein-stabilized emulsions indicated advanced oxidation. Comparison with the physically more stable emulsions stored at 6 °C pointed to the role of co-oxidation between proteins and lipids in coalescence of oil droplets and increase in droplet size. Emulsions stabilized with amaranth proteins showed higher resistance to oxidation compared to quinoa protein containing emulsions.