In Chile, the most cultivated avocado varieties are Hass and Negra de la Cruz. The increase in the production of fast food preparations, salads, and avocado oil has generated large amounts of seeds and husks as waste, which may constitute a possible new source of bioactive compounds, of great interest to the food and pharmaceutical industry. Therefore, the objective of this study was to determine different nutritional, biochemical, antimicrobial, and physical properties of the SH and SNC seeds grown in Chile. In SH and SNC, their nutritional composition, lipophilic components, and total phenols (PTs) were determined. The antioxidant and antibacterial activity of extracts were measured in different solvent combinations. In addition, the color change of seeds (ΔE) during the browning, the mechanical resistance to the cut, and their thermal transitions by differential calorimetry (DSC) were determined. The results indicated that SH has a higher protein content and lipophilic components. In the ethanol extract, SNC showed greater antiradical activity and is an inhibitor of Gram (+) bacteria. The SNC browning given by ΔE was greater and adjusted well to kinetic and enzymatic models. The physical analyses of the seeds indicated that SNC presented higher cut resistance and lower transition temperature (Tg) with a lower thermal fusion of its lipids, which would be due to its higher unsaturated composition. These properties of SH and SNC can be useful for the agrifood, pharmaceutical, and chemical industries.