Firms are increasingly using science-based partnerships to organize for open innovation. To attain outcomes like innovations and high-quality research, science-based partnerships usually consist of multiple short-term R&D projects in which partners work closely together. However, partners often find it difficult to achieve jointly beneficial outcomes. This study explores a science-based partnership and three of its R&D projects to gain multilevel insights into how partners through alignment practices can achieve jointly beneficial outcomes. We find that partner alignment happens through practices that are influenced by structured coordination at the partnership level and mainly unstructured coordination at the project level. Our findings contribute to the literature on open innovation and coordination mechanisms by providing a multilevel view of the dynamic process of partner alignment and showing how it influences outcomes in partnerships. Our findings provide insights into why some open innovation projects fail while other projects succeed, and they have important managerial implications related to how partners in R&D projects should align to attain outcomes.