Background: Very little is known about the practice-oriented challenges and mitigation strategies for effective and efficient translation of informed consent and study prioritization in times of a pandemic. This stakeholder interview study aimed to identify the full spectrum of challenges and mitigation strategies for informed consent and study prioritization in a pandemic setting. Methods: We performed semi-structured interviews with German stakeholders involved in human subject research during the COVID-19 pandemic. We continued sampling and thematic text analysis of interview transcripts until thematic saturation of challenges and mitigation strategies was reached. Results: We conducted 21 interviews with investigators, oversight bodies, funders and research support units. For the first topic informed consent we identified three main categories: consent challenges, impact of consent challenges on clinical research, and potential response strategies for consent challenges. For the second topic prioritization of trials, we identified two main categories: need for prioritization of clinical studies and potential response strategies for prioritization of clinical studies. All main categories are further specified with subcategories. A supplementary table provides original quotes from the interviews for all subcategories. Discussion: Mitigation strategies for challenges with informed consent and study prioritization partly share common ground. High quality procedures for study prioritization, for example, seem to be a core mitigation strategy in dealing with informed consent challenges. Especially in a research environment with particularly high uncertainty regarding potential treatment effects and further limitations for valid informed consent should the selection of clinical trials be very well justified from a scientific, medical, and ethics viewpoint.