Cannabis sativa (hemp) seeds are considered a functional food for their favorable contents of essential fatty acids, proteins and antioxidants. Beyond phenolics and carotenoids, the bioactivity of proteins has recently been investigated. However, plant genotype and environmental conditions can affect quantity and quality of macronutrients and phytochemicals in seeds, influencing their nutraceutical properties. In this study, the effects of plant variety and seed origin on the protein profile and antioxidant activity of hemp seeds were evaluated. Seeds from two cultivars, Secuieni Jubileu and Finola, were harvested from a mountain field located in Italy and compared with reference seeds used for sowing. Albumin and globulin extracts were obtained using the Osborne method and their antioxidant power was assayed (DPPH and ABTS methods). A matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry method was developed for protein fingerprinting analysis. Albumins from seeds of the mountain site showed higher radical scavenging activity and compounds of lower molecular weight than reference seeds, suggesting a role of proteins in the observed bioactivity. The MALDI-TOF method discriminated samples according to origin and variety, highlighting changes in the protein profile and identifying signals which could be used as markers of hemp cultivars.