This scoping review maps research ethics and integrity challenges and best practices encountered by research actors in the DACH countries (Germany, Austria, and Switzerland), including researchers, funders, publishers, research ethics committees, and policymakers, during the COVID-19 pandemic. The COVID-19 pandemic brought research and, in turn, research ethics and integrity, into public focus. This review identified challenges related to changing research environments, diversity in research, publication and dissemination trends, scientific literacy and trust in science, recruitment, research redundancy and study termination, placebo and human challenge studies, data management, and informed consent. These challenges are linked to two crucial factors: first, actors in the DACH research ecosystem lacked a sound knowledge base to assess the risks and benefits of research during the COVID-19 pandemic. Second, researchers in the DACH region faced pressure from policymakers, funders, and the public to generate relevant, timely, and consistent findings to mitigate the impacts of the COVID-19 pandemic. In addition, this review highlights best practices to mitigate the effects of future crises on research ethics and integrity, including enhanced cooperation among actors, continuous ethics assessments, and support for public scientific literacy.