Conceptual design has frequently been regarded as an unnecessary step when talking of a facility design, but, on the contrary, it should be seen as a key step to have a compliant facility suitable for the operations to be conducted. A good conceptual design may lead to a well thought and managed facility…or not, but an unsatisfactory conceptual design will for sure lead to a defective facility, non-compliant or very inefficient. Therefore, it is extremely important to dedicate the time to execute this process, and produce the correct design for the operations and products for each facility. Divided into two chapters, this article explores the relevance of this stage in the development of a new pharmaceutical plant, their impact in the future production performance and the keys in the design phase defining the feasibility of a tailor-made fit pharmaceutical plant. This second part of the article addresses the key points of the management of subsequent phases following the information collection, such as the product categorization, capacity study, Site Master Plan (SMP), layout development, classifications & over pressures and flows review.