Fruit processing contributes significantly to the agricultural exportation of the Amazonian; however, it generates large amounts of solid waste, despite its high content of bioactive compounds and nutritional properties, and they are discarded in the environment. Therefore, in order to add economic value and potential reuse of agro-industrial by-products from cocoa, cupuassu, pracaxi, and tucumã, we investigated the chemical characteristics of the seed by-product resulting from the industrial extraction of these oils. The investigation of the nutritional and chemical composition of by-product was submitted to green extraction, besides other qualitative and quantitative techniques for the characterization of the main bioactive compounds. The extracts obtained from these by-products had a significant total polyphenol content and antioxidant activity. HPLC analysis identified and quantified some flavonoids present in these by-products (gallic, caffeic and protocatechuic acid, epigallocatechin-3-gallate, epicatechin, catechin, and quercetin). The oil from these species is widely used in the treatment of skin scarring and inflammation and is also used by the cosmetic industry. These results show that these by-products have a great potential for use, since they still have bioactive substances in their composition, which could alternatively be used in the pharmaceutical, cosmetic, or food industries.