Background: Smartphone self-monitoring through ecological momentary assessment (EMA) provides insights into the daily lives of people in psychiatric treatment and has the potential to improve their care. Currently, no clinical tools are available that help clients and clinicians with creating personalized EMA diaries and interpreting the gathered data. Integration of EMA in treatment is therefore difficult.Objective: To develop a web-based application for personalized EMA in routine psychiatric care, in close collaboration with all stakeholders (i.e., clients, clinicians, researchers, and software developers). Methods: We engaged 52 clients with mood, anxiety, and/or psychotic disorders and 45 clinicians (psychiatrists, psychologists, and psychiatric nurses) in interviews, focus groups, and usability sessions. We used human-centered design principles to determine important requirements for the web-app and designed high-fidelity prototypes that were continuously reevaluated and adapted. Results: The iterative development process resulted in PETRA (PErsonalized Treatment by Real-time Assessment), which is a scientifically grounded web-app for the integration of personalized EMA in clinical care. PETRA includes a decision aid to support clients and clinicians with constructing personalized EMA diaries, an EMA diary item repository, a text-message-based diary delivery system, and a feedback module for visualizing the gathered EMA data. PETRA is integrated in electronic health record (EHR) systems to ensure ease-of-use and sustainability, and adheres to privacy regulations.Conclusions: PETRA was built to fulfill the needs of clients and clinicians for a user-friendly and personalized EMA tool embedded in routine psychiatric care. PETRA is unique in this co-development process, its extensive yet user-friendly personalization options, its integration in EHR systems, its transdiagnostic focus, and its strong scientific foundation in the design of EMA diaries and feedback. The clinical effectiveness of integrating personalized diaries via PETRA into care awaits further research. As such, PETRA paves the way for a systematic investigation into the utility of personalized EMA for routine mental health care.