The emergence of transgenic crops as alternative production hosts presents downstream process developers with unique challenges. A generalized bioprocessing scheme includes harvesting the plant tissue, tissue grinding, extraction of the target protein into an aqueous medium, clarification, and purification. Each plant host contains a unique and variable set of matrix components (proteins, lipids, phenolics, carbohydrates, alkaloids, etc.) that must be removed during purification of the target protein. The presence and quantity of these impurities in the extract vary significantly between types of host systems (seed, tubers, and leaves) and extraction conditions. In some cases, extraction conditions such as solid-to-liquid ratio, pH, ionic strength, and homogenization/disintegration method could be used to reduce the amount of host-derived impurities that may interfere with subsequent purification steps. In other situations, specific impurities (e.g. protease, phenolics) dictate operating conditions and reduce process options for extraction and recovery steps. The recent paradigm shift toward the use of contained systems such as aquatic plants and plant cell culture may introduce new variables to downstream processing. Key tasks in downstream process development are to identify critical extract impurities, evaluate their impact on selected recovery and purification steps and rationally design an integrated process that exploits potential advantages of each host system. This presentation will compare strategies currently employed for the downstream processing of seed and green tissue expressed recombinant proteins. Bottlenecks and further developments in recovery and purification technologies for plant-derived proteins will be addressed.