The increase in the consumption of food products and the management of food waste have endangered the sustainability of the food sector. The need to move forward on the European bioeconomy requires to evaluate waste valorization strategies, to convert a non-valorized resource into a high-added value production in the market. In this regard, the focus of this research article is the valorization of orange peel and tomato seed wastes to produce bioactive compounds, such as carotenoids. Various extraction technologies have been analyzed, from the most conventional (solvent extraction), to emerging alternatives (including ultrasound-assisted extraction, microwave-assisted extraction and subcritical water extraction), providing a total of seven scenarios. Life Cycle Assessment methodology has been used for assessing the environmental sustainability of all the scenarios, combined with techno-economic analysis to evaluate its feasibility and also to provide an eco-efficiency evaluation. The results show that energy optimization is key to improve the profiles obtained, as well as to increase production capacity, as it is directly related to both economic and environmental viability. In general terms, orange peel valorization scenarios with emerging technologies are the most profitable and suitable, given the higher benefits and lower impacts compared to tomatoe valorization. The research developed has shown that the recovery of bioactive compounds from unusable wastes from the food and agricultural sectors is effective, and the outcomes could be used as a guide to stakeholders and entrepreneurs to where to focus to enhance the potential of the tomato and orange harvesting and processing activities.