When trying to commercialize, science‐based ventures often face contradicting institutional logics. While stakeholders appreciate scientific ability, they also increasingly demand concessions to a commercial logic focusing on efficiency and profit. To satisfy stakeholders, science‐based ventures must adapt their organizational identity to include the commercial logic. The study investigates this challenge, relying on a 24‐month in‐depth study of a venture in the photonics industry. Based on the findings, I developed a process model that outlines how the logics shift from compatibility to incompatibility during the adoption process, thereby causing the organizational identity to fragment. The paper contributes to research streams on organizational identity processes, dynamics of institutional logics in organizations, and scaling of science‐based ventures.