With the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), scientists worldwide encountered substantial obstacles. The German National Pandemic Cohort Network (NAPKON) was established in the fall of 2020 to make optimal use of available resources and coordinate research initiatives to address the coronavirus disease 2019 (COVID-19) pandemic. We evaluated the initial setup phase of NAPKON as a representative case for multicenter research efforts in Germany, with particular attention to the difficulties encountered and areas for potential improvement when linking 59 university and non-university study sites. We reviewed the ethics application procedures involving 121 ethics submissions, analyzing processing times, reviewer comments, and final decisions. Activation of study sites and patient enrollment activities were examined in relation to SARS-CoV-2 infection incidence rates. Across all initial ethics applications, the median time to a favorable ethics vote was under 2 weeks, and 30 of the study sites (65%) successfully integrated into NAPKON within 3 weeks per site. The use of electronic submission methods instead of traditional postal delivery (9.5 days (Q1: 5.75, Q3: 17) vs. 14 days (Q1: 11, Q3: 26), P-value = 0.01), along with acceptance of the lead ethics vote, markedly shortened the overall ethics review timeline. On average, each participating center recruited 37 patients over the 14-month monitoring period, although enrollment volumes varied widely across health care sectors. A clear positive association was identified between enrollment success and both COVID-19 incidence and hospitalization rates. The findings illustrate both the limitations and the advantages of Germany’s decentralized federal research framework. Implementing digital ethics submission platforms, recognizing a primary ethics decision, and establishing uniform procedural standards can promote greater consistency and accelerate the launch of studies in emergency pandemic situations.