This chapter examines the role of resilience in European R&D collaborative projects through the application of a complex theory framework. This chapter highlights how collaborative innovation is influenced by perturbations—unforeseen disruptions that can significantly impact project outcomes—and explores how resilience can be developed to overcome such challenges. Using the case of the LOCUTIOS project, the study analyzes two major perturbations that the project encountered, and the strategies implemented to navigate them. The research underscores the importance of governance, equivocality, and organizational learning in shaping resilient behaviors. This chapter applies a Complex Adaptive Systems (CAS) model to illustrate the dynamic and non-linear interactions between these domains and their impact on project stability and success. The findings emphasize the need for adaptive governance strategies and collaborative learning approaches to manage uncertainties and ensure the success of R&D initiatives.