Background: The interruption of the activity of population-based organized colorectal cancer (CRC) screening programs due to the COVID pandemic may have affected their results in terms of the detection of preneoplastic lesions and CRC. We evaluated the impact of the COVID pandemic on the delays, participation, adherence to colonoscopies, lesions detected, and CRC stage at diagnosis in a CRC screening program. Methods: We analyzed all the invitations between 1 January 2019 and 31 December 2021. We defined the pandemic period as the period after 12 March 2020. We calculated the delay intervals (successive and all rounds), the rates of participation, adherence to colonoscopy after a positive fecal immunochemical test (FIT), and the diagnostic yield of colonoscopy, specifically of CRC and colorectal neoplasia (CRC and/or adenoma), as well as the CRC stage at diagnosis. Results: In the period analyzed, 976,187 invitations were sent (61.0% in the pandemic period), 439,687 FIT were returned (62.4% in the pandemic period) and 23,092 colonoscopies were performed (59.1% in the pandemic period). The colonoscopies were normal in 7378 subjects (32.4%) and CRC was detected in 916 subjects (4.0%). In successive rounds, the delay increased significantly by seven months during the pandemic period (p < 0.001). In all the invitations, the delay from the invitation to the colonoscopy increased significantly by 8 days (p < 0.001). Once adjusted for the confounding variables, the participation in the screening program increased significantly (OR = 1.1; 95% CI = 1.09–1.11), with no changes in the adherence to colonoscopy (OR = 0.9; 95% CI = 0.8–1.0). We found no differences in the diagnostic yield of colonoscopy in terms of CRC (OR = 0.90; 95% CI = 0.78–1.02) or colorectal neoplasia (OR = 0.98; 95% CI = 0.92–1.03) detection. Finally, we found no differences in the CRC stage at diagnosis (p = 0.2). Conclusions: Although the interruption of the CRC screening program due to the COVID pandemic increased the delays, it did not reduce participation, adherence to colonoscopy, or the diagnostic yield of colonoscopy.