Background: During the COVID-19 pandemic, the Flemish colorectal cancer (CRC) screening program (by fecal immunochemical test, FIT) was suspended and non-urgent medical procedures were discommended. This study estimates how this impacted diagnostic colonoscopy (DC) scheduling after a positive FIT and the interval between both in 2020. Methods: An online survey was sent to participants in the Flemish CRC screening program with a positive FIT but without a DC to explore the possible impact of COVID-19 on the scheduling of a DC. Self-reported survey results were complemented with objective data on DC compliance and the interval between FIT and DC. Results: In 2020, DC compliance was 4–5% lower than expected (for 3780 positive FITs no DC was performed). In February–March 2020, the median time between a positive FIT and DC significantly increased. Survey participants reported fear of COVID-19 contamination, perception to create hospital overload, delay in non-urgent medical procedures (on government advice) and not being sure a DC could be performed as contributing reasons. Conclusions: On top of a 3% lower participation, the COVID-19 pandemic further increased existing DC non-compliance and the positive FIT–DC interval. The survey confirmed the crucial role of COVID-19 in the decision not to plan a DC.