Background: Digital innovations in medicine are disruptive technologies that can change the way diagnostic procedures and treatments are delivered. Such innovations are typically designed in teams with different disciplinary backgrounds. This paper concentrates on 2 interdisciplinary research teams with 20 members from the medicine and engineering sciences working jointly on digital health solutions. Objective: The aim of this paper was to identify factors on the individual, team, and organizational levels that influence the implementation of interdisciplinary research projects elaborating on digital applications for medicine and, based on the results, to draw conclusions for the proactive design of the interdisciplinary research process to make these projects successful. Methods: To achieve this aim, 2 interdisciplinary research teams were observed, and a small case study (response rate: 15/20, 75%) was conducted using a web-based questionnaire containing both closed and open self-report questions. The Spearman rank correlation coefficient was calculated to analyze the quantitative data. The answers to the open-ended questions were subjected to qualitative content analysis. Results: With regard to the interdisciplinary research projects investigated, the influencing factors of the three levels presented (individual, team, and organization) have proven to be relevant for interdisciplinary research cooperation. Conclusions: With regard to recommendations for the future design of interdisciplinary cooperation, management aspects are addressed, that is, the installation of a coordinator, systematic definition of goals, required resources, and necessary efforts on the part of the involved interdisciplinary research partners. As only small groups were investigated, further research in this field is necessary to derive more general recommendations for interdisciplinary research teams.