Successful translation of promising preclinical findings into clinical application remains challenging. To address the rising concerns of failing clinical trials and the resulting economic, social, and ethical consequences, preclinical confirmatory studies have been proposed to generate sufficiently robust evidence for guiding the decision-making process. In a unique funding call, 17 studies in Germany aimed to confirm exploratory findings across various biomedical research fields in a rigorously planned and executed multi-laboratory set-up. Alongside these preclinical research projects, a meta-research project was funded to provide methodological support and collectively investigate confirmatory study design and experimental outcomes. After the first four-year funding period, an in-person workshop brought together representatives from the preclinical confirmatory studies to discuss lessons learned. We summarize the outcomes of these stakeholder discussions, highlight common pitfalls, and propose optimization strategies for experimental set-up and project coordination. As a result, we advocate for new roles—such as preclinical research coordinators—and improved rules and regulations in preclinical research to facilitate large-scale academic research projects. Moreover, we highlight that diverse stakeholders must collaborate to effectively integrate confirmatory multi-laboratory studies into the preclinical research ecosystem.