The pharmaceutical and specialty chemical industries are challenged with the requirement of faster time-to-process to meet market demands. Here, Modular Plants made up of predesigned process equipment assemblies (PEAs) are advantageous. Moreover, equipment-based Digital Twins of these modules can further reduce the time-to-process when combined with methods such as Quality by Design (QbD) and model-based design of experiments (MBDoE) to reduce uncertainty. This paper presents a lab scale-based workflow using an equipment-based Digital Twin, which applies QbD and MbDoE methods to identify the Design Space in the lab scale which can be transferred to production scale equipment as part of a Digital Twin based workflow for scale-up in Modular Plants.