Federally Qualified Health Centers (FQHC) provide preventive health services such as colorectal cancer (CRC) screening to low-income and underinsured individuals. Overall CRC screening participation in the United States declined during the COVID-19 pandemic and recovered by 2021; however, trends in underresourced settings are unknown. Using Uniform Data System data from 2014 to 2022, we assessed trends in FQHC CRC screening rates nationally, in California, and in Los Angeles County and determined clinic-level factors associated with recent screening rate changes. For each FQHC, we calculated the screening rate change from 2019 to 2020, 2020 to 2021, and 2020 to 2022. We used mixed-effects linear regression to determine clinic-level characteristics associated with each screening rate change. Across all FQHC (n = 1,281), 7,016,181 patients were eligible for CRC screening in 2022. Across the United States and in California, median screening rates increased from 2014 to 2019, severely declined in 2020, and failed to return to prepandemic levels by 2022. Both nationally and in California, CRC screening declined most dramatically from 2019 to 2020 in FQHC serving majority Hispanic/Latino patients or a high proportion of patients experiencing homelessness. From 2020 to 2022, screening rates did not recover completely in US FQHC, with disproportionate recovery among FQHC serving majority non-Hispanic Black patients. CRC screening rates at FQHC did not return to prepandemic levels by 2022, and recovery varied by FQHC patient characteristics. Tailored interventions addressing low and decreasing CRC screening rates in FQHC are urgently needed to mitigate worsening CRC disparities.