Plant-based medicines have an important role in the lives of millions of people. The ancient knowledge of the use of plants as medicines has led to the discovery of many important western pharmaceuticals, and the popularity of whole plant preparations for a range of therapeutic applications is growing rapidly. However, there are many challenges in the production of plant-based medicines, many of which put both the consumer and the plant populations at risk. Modern biotechnology can be optimized to mass-produce plants of specific chemical composition for use as particular treatments and applications. In this review, we have used one of the most important medicinal plant genera, Scutellaria, as a model to assess the potential of applications of biotechnology for the improvement of medicinal plants.