Plants are now gaining widespread acceptance as a general platform for the large-scale production of recombinant proteins. The principle has been demonstrated by the success of a diverse repertoire of proteins, with therapeutic molecules showing the most potential for added value. Over the past 10 years, several efficient plant-based expression systems have emerged. However, a number of issues remain to be addressed before plant bioreactors can be accepted and adopted widely in preference to the established microbial and mammalian platforms. Overcoming bottlenecks imposed by low yields, poor and inconsistent product quality and difficulties with downstream processing are the most important goals for researchers working in this field. The achievement of these goals is conditional on the development of extraction and processing steps that comply with GMP standards, including extensive quality assurance and control procedures. Such rigorous and validated standards should be combined with measures applied earlier in production to ensure product sustainability and quality, such as the use of master seed banking procedures. Moreover, there are several further challenges concerning topics of environmental impact, biosafety and risk assessment, which reflect the release of transgenic plants, as well the safety of the plant-derived products themselves. We are facing a growing demand for protein diagnostics and therapeutics, but lack the capacity to meet those demands using established facilities. A shift to plant bioreactors may, therefore, become necessary within the next few years, making it more imperative that the technical and regulatory limitations are addressed and solved. The production of pharmaceutical proteins in plants will only realize its huge potential if the products are provided at consistent high quality levels, allowing the delivery of clinical grade proteins that will gain regulatory approval and which can be used routinely in clinical trials.