Seed meals and cakes, deriving from minor oilseed crops, represent interesting co-products for the presence of a high content of proteins and bioactive compounds that could be successfully explored as valuable plant-derived feedstocks for food and non-food purposes. In this contest, flaxseed (Linum usitatissimum L.) and camelina (Camelina sativa (L.) Crantz) are becoming increasingly important in the health food market as functional foods and cosmetic ingredients. Thus, this study aimed to evaluate the effect of genetic characteristics and cultivation sites on the chemical features of seed meals deriving from two flaxseed varieties (Sideral and Buenos Aires) and a camelina cultivar (Italia), cultivated in Central and Northern Italy (Pisa and Bologna). The content of total phenols and flavonoids, seed oil, proteins and fatty acids have been evaluated, together with the chemical profiles of flaxseed and camelina meals. In addition, radical-scavenging activity has been investigated. All the examined seed meals resulted as rich in bioactive compounds. In particular, flaxseed meal is a good source of the lignan secoisolariciresinol diglucoside (SDG) and hydroxycinnamic acid glucosides, while camelina meal contains glucosinolates and quercetin glycosides. Furthermore, all extracts exhibited a very strong radical-scavenging activity, that make these plant-derived products interesting sources for food or cosmetic ingredients with health outcomes.