Tree nuts are rich in unsaturated fatty acids and nuts have human health benefits. It is important that postharvest processing does not negatively impact nut fatty acid composition and nut oil quality. Canarium indicum (Burseraceae) is an indigenous tree in the southwest Pacific that produces edible nuts. Canarium nuts are rich in oil (>70%), protein (14%), mineral nutrients and vitamin E. Domestication of Canarium nuts has been a priority in several Pacific countries. A centralised processing factory has been established in Papua New Guinea to produce high-quality Canarium products. We investigated the effects of freezing (frozen vs. fresh) on the fatty acid composition, peroxide value (PV) and free fatty acid (FFA) content of kernels. Freezing nuts did not change the total saturated and total unsaturated fatty acid of kernels compared with fresh kernels. Frozen kernels had significantly lower FFA than fresh kernels. We also explored the effects of roasting and roasting after dipping in salt-water solution on oil oxidation of kernels. The treatments included roasting at 150°C for 10 min, roasting at 150°C for 30 min after dipping in salt-water solution and unroasted. Roasted kernel with or without salt solution dipping had significantly higher PV than unroasted kernels. These results of these studies have led to the establishment of factory protocols for producing Canarium products with high food-quality and food-safety standards.