In a period of almost three decades, Uruguay built a forest industry based on fast-growing and short rotation eucalypts and pines plantations, beside a policy planned native forests conservation. The government is currently boosting a transition to a bioeconomy that considers the potential of new products, processes, supply chains and markets conformation of both plantations and native forests. Secondary metabolites of native trees hold historically a great potential as non-wood forest products but have remained poorly investigated. This work presents advances in bioprospecting, identification, separation and chemical characterization of secondary metabolites of three forest trees, as raw materials for innovative non-wood forest products. The research initiated in 2013 through an agreement between the National Agricultural Research Institute and the Faculty of Chemistry of the Republic University of Uruguay. The activities focused on:(i) the bioprospecting of three species (Prosopis affinis, Prosopis nigra and Quillaja brasiliensis) and (ii) the identification and chemical characterization of selected secondary metabolites. Chemical analysis were realized using HPLC and mass spectrometry. Saponins, galactomannans and alkaloids were separated and characterized at laboratory scale. The next steps point to biomass production to enable an industrial pilot scale phase and economic studies on supply chains and markets conformation.