BackgroundIn 2017, the San Francisco Cancer Initiative (SF CAN) established the Colorectal Cancer (CRC) Screening Program to provide technical assistance and financial support to improve CRC screening processes, and outcomes in a consortium of community health centers (CHCs) serving low-income communities in San Francisco. The purpose of this study was twofold: to evaluate the perceived influence of the support provided by the CRC Screening Program’s Task Force on CRC screening processes and outcomes in these settings and to identify facilitators and barriers to SF CAN-supported CRC screening activities before and after the onset of the COVID-19 pandemic.MethodsSemi-structured key informant interviews were conducted with consortium leaders, medical directors, quality improvement team members, and clinic screening champions. Interviews were audio-recorded, professionally transcribed, and analyzed for themes. The Consolidated Framework for Implementation Research (CFIR) was used to develop the interview questions and organize the analysis.ResultsTwenty-two participants were interviewed. The most commonly cited facilitators of improved screening processes included the expertise, funding, screening resources, regular follow-up, and sustained engagement with clinic leaders provided by the task force. The most salient barriers identified were patient characteristics, such as housing instability; staffing challenges, such as being understaffed and experiencing high staff turnover; and clinic-level challenges, such as lack of ability to implement and sustain formalized patient navigation strategies, and changes in clinic priorities due to the COVID-19 pandemic and other competing health care priorities.ConclusionsImplementing CRC screening programs in a consortium of CHCs is inherently challenging. Technical assistance from the Task Force was viewed positively and helped to mitigate challenges both before and during the pandemic. Future research should explore opportunities to increase the robustness of technical assistance offered by groups such as SF CAN to support cancer screening activities in CHCs serving low-income communities.Supplementary InformationThe online version contains supplementary material available at 10.1186/s43058-023-00439-x.