The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) created unprecedented challenges for research worldwide. To coordinate efforts and optimize resources in response to the COVID-19 pandemic, Germany established the National Pandemic Cohort Network (NAPKON) in autumn 2020. This study evaluates the initial implementation of NAPKON as a model for multicenter research, focusing on the difficulties and opportunities involved in linking 59 university and non-university study sites. We reviewed 121 ethics submissions, analyzing their processing times, feedback, and outcomes. In addition, study site activation and patient recruitment were assessed in relation to regional SARS-CoV-2 infection rates. Initial ethics approvals were typically granted in under two weeks, and 65% of study sites (30 centers) became operational within three weeks. Using electronic submissions instead of postal applications (9.5 days [Q1: 5.75, Q3: 17] vs. 14 days [Q1: 11, Q3: 26], p = 0.01) and accepting a primary ethics vote significantly reduced approval timelines. Across the observation period of 14 months, each center enrolled a median of 37 patients, though rates varied considerably depending on the healthcare sector. Recruitment success was positively associated with both COVID-19 case numbers and hospitalization rates. Overall, the findings underscore both the challenges and advantages of Germany’s federated research system, suggesting that digital ethics tools, primary ethics vote adoption, and standardized procedures can facilitate faster and more uniform study initiation during a public health crisis.