The study examined the physical, morphological, thermal, techno-functional, and rheological properties of two apple seed cultivars viz: red delicious (RD) and golden delicious (GD). Physical properties showed that red delicious seeds were significantly (p≤0.05) different in width, geometric mean diameter, arithmetic mean diameter, volume, and surface area than golden delicious seeds. The proximate composition of RD seed flour showed a higher amount of crude protein and fat content than GD seed flour. RD seed flour was significantly different in L*, a*, b* values, bulk density, water/oil absorption capacity and the emulsifying ability than GD seed flour. From particle size analysis it was possible to found that GD was significantly (p≤0.05) lower than RD flour macromolecules. Scanning electron micrographs showed oval/spherical starch granules of small size embedded in a continuous protein matrix. Thermograph revealed exothermic transition enthalpy for both RD and GD seed flour, which indicates a high energy requirement for crystallite melting. The rheological assays revealed high elastic modulus (G′), of seed flours that will help in modifying the texture of foods. This study suggests the potential of apple seeds in the formulation of protein-enriched foods to combat malnutrition while contributing to the reduction in industrial wastage.