High-added value biological compounds (BACs) from herbal and plant sources, such as essential oils (EO), antioxidants and volatile compounds, often exhibit remarkable features, ranging from nutritive and medicinal properties, as well as antimicrobial and antioxidant activities, which can be exploited in the production of functional foods. However, most BACs exhibit low water solubility, strong off-flavors/odors, and are generally unstable and easily degraded under common processing and storage conditions. Encapsulation is a technology that enables the delivery in food systems, the protection, as well as the controlled and targeted release of BACs. The aim of this review is to summarize the most important information for encapsulation of natural extracts using unconventional technologies. Encapsulation is an excellent choice to stabilize BACs, and in particular EOs, and mask their strong flavors and odors. In particular, spray drying is one of the most economic and common encapsulation technologies. However, the challenges of reducing the operating costs, of developing high-throughput processes, of minimizing the use of organic solvents, and of increasing the level of functionality of the encapsulation systems are driving the research towards the implementation of innovative strategies and non-conventional methods, which incorporate the concepts of Green Food Processing. Display omitted •Biological compounds from herbal and plant sources have remarkable features.•Encapsulation is a technology that enables their delivery in food systems.•Encapsulation of natural extracts can be achieved by unconventional technologies.