In today’s linear economy, waste streams, environmental pollution, and social−economic differences are increasing with population growth. The need to develop towards a circular economy is obvious, especially since waste streams are composed of valuable compounds. Waste is a heterogeneous and complex matrix, the selective isolation of, for example, polyphenolic compounds, is challenging due to its energy efficiency and at least partially its selectivity. Extraction is handled as an emerging technology in biorefinery approaches. Conventional solid liquid extraction with organic solvents is hazardous and environmentally unfriendly. New extraction methods and green solvents open a wider scope of applications. This research focuses on the question of whether these methods and solvents are suitable to replace their organic counterparts and on the definition of parameters to optimize the processes. This review deals with the process development of agro-food industrial waste streams for biorefineries. It gives a short overview of the classification of waste streams and focuses on the extraction methods and important process parameters for the isolation of secondary metabolites.