New generations of biorefinery combine innovative biomass waste resources from different origins, chemical extraction and/or synthesis of biomaterials, biofuels, and bioenergy via green and sustainable processes. From the very beginning, identifying and evaluating all potentially high value-added chemicals that could be removed from available renewable feedstocks requires robust, efficient, selective, reproducible, and benign analytical approaches. With this in mind, green and sustainable separation of natural products from agro-industrial waste is clearly attractive considering both socio-environmental and economic aspects. In this paper, the concepts of green and sustainable separation of natural products will be discussed, highlighting the main studies conducted on this topic over the last 10 years. The principal analytical techniques (such as solvent, microwave, ultrasound, and supercritical treatments), by-products (e.g., citrus, coffee, corn, and sugarcane waste) and target compounds (polyphenols, proteins, essential oils, etc.) will be presented, including the emerging green and sustainable separation approaches towards bioeconomy and circular economy contexts.