Modular plants built from process equipment assemblies (PEAs) provide a promising solution to challenges like increasing requirements of flexibility and faster time to market. To leverage the potential in processes under good manufacturing practice (GMP) conditions new methods are required to support the process validation in modular plants. In this paper, we present an integrated approach to Quality by Design and Process Performance Qualification between lab and production scale in modular plants applying the Product-Process-Resource model by Bamberg et al. (2021). Furthermore, we reformulate the Extended Flexibility Analysis by Ochoa et al. (2021) adapting the terminology to the Quality by Design context and adding the control inputs in the form of the CPPs to the optimization problem. The problem is solved by means of a grid search algorithm. The approach is studied and illustrated in a simulation-based case study with a simple reaction system.