Abstract <p>Community coalition approaches such as Communities That Care (CTC) are regarded as key strategies for translating prevention science into community-level improvements in youth outcomes. It was shown that CTC improves three system transformation outcomes. The present study aimed to conceptually replicate these findings in the German context under the highly unusual real-world implementation constraints imposed by the COVID-19 pandemic. A non-randomized community trial was carried out (2020–2023) in 22 a priori matched community-pairs from four German states. In an open cohort design, community key informants were surveyed at two time points. A total of 318 key informants from 18 ICs (<i>n</i> = 180) and 11 CCs (<i>n</i> = 138) were included in the open-cohort analyses. Outcomes included (1) adoption of a science-based approach to prevention (primary outcome), (2) sectorial collaboration (SC) for prevention, and (3) prevention collaboration (PC). Three-level mixed models were used to analyse changes over time. In addition to replicating the original binary comparison of intervention communities (ICs) and comparison communities (CCs), analyses were extended to account for heterogeneity in implementation progress across ICs resulting from pandemic-related implementation disruptions. At baseline, ICs showed significantly higher levels of SC than CCs (<i>γ</i> = 0.383, SE = 0.124, <i>p</i> = .003), whereas no significant baseline differences were observed for Adoption or SC. Compared with CCs, ICs showed a non-significant increase in the primary outcome (<i>b</i> = 0.272, SE = 2.306,<i> p</i> = .906) and PC (<i>γ</i> = 0.78, SE = 0.121, <i>p</i> = .523), whereas SC showed a non-significant decrease over time in ICs relative to CCs (<i>γ</i> = − 0.193, SE = 0.118, <i>p</i> = .107). Implementation progress was not significantly associated with changes in the primary outcome (<i>b</i> = 0.401, SE = 0.929, <i>p</i> = .666), SC (<i>γ</i> = 0.082, SE = 0.100, <i>p</i> = .415), or PC (<i>γ</i> = 0.018, SE = 0.094, <i>p</i> = .847). Sensitivity analyses based on panel data and non-imputed datasets yielded largely comparable findings. No significant effects on system transformation were observed. However, given the limited implementation progress under COVID-19 conditions, longer follow-up may be needed to assess whether CTC can achieve system-level change in Germany.&#xa0;</p> Trial registration <p>This study was registered with German Clinical Trial Register: DRKS00022819 on Aug 18, 2021.</p>