Advancement in sensor technologies driven by the FDA’s Process Analytical Technologies framework and increasingly cheap and easy access to powerful cloud computing is creating an opportunity for a digital transformation in cell and gene therapy bioprocessing. This includes the prospect of advanced process control, using connected, digitally enabled soft sensor technologies to monitor critical process variables and adapt the process in real-time to maintain product quality. This type of transformation brings with it numerous challenges, not least of which is how to handle and process the large amount of complex data required to enable informed process decision making. Here we look at how a Quality-by-Design framework for digitized manufacturing could be implemented with a particular focus on the challenges of modelling and analyzing the complex data required to control dynamic processes. Going forward, this framework, which bring together physical systems alongside digital infrastructure could act as an enabler for concepts such as Industry 4.0 within the cell and gene therapy sector.