Continuous flow chemistry has many well-established advantages, including its facile automation, that make it an attractive technology for the rapid development and synthesis of target molecules. In this chapter, we highlight recent examples of automated continuous flow systems capable of chemical reaction optimization through the integration of process analytical technology and optimization algorithms. We then transition to describing automated continuous flow manufacturing platforms engineered for small molecule synthesis, namely pharmaceutical production. Such systems have realized capabilities in complex multistep synthesis and downstream operations like purification, crystallization and formulation steps.