In this study, the structural, antioxidant, antidiabetic, antiobesity, and antimicrobial properties of two himalayan apple seed varieties (red delicious (RD) and golden delicious (GD) was investigated. The morphological characterization of seed flours revealed starch granules of varying shapes and dimensions with agglomerated protein bodies. XRD shows high crystallinity, while as the FTIR spectroscopy indicates high intensity of bands at 1639 cm−1 and 1528 cm−1 in RD seed flour, which are characteristics of amine I and II. Besides, higher phenolic content (12.30 mgGAE/g) was observed in RD which provided excellent results for antioxidant capacity as measured by DPPH radical scavenging capacity assay (49.2–86.9%), reducing power, and inhibition of lipid peroxidation (38.2–86.3%). Consequently, RD flour exhibited higher α-glucosidase (34.5–86.6%) and pancreatic lipase (24.9–72.6%) inhibition. The antimicrobial study revealed that both flour samples inhibit the growth of B. subtilis and S. aureus. This study therefore suggests the possible use of apple seeds in different food formulations.