Colonoscopy quality, as measured by adenoma detection rates, varies widely across providers and is inversely related with patients’ post-colonoscopy cancer risk. This has unknown consequences for the benefits of faecal immunochemical testing (FIT) versus primary colonoscopy screening for colorectal cancer. Using an established microsimulation model, we predicted the lifetime colorectal cancer incidence and mortality benefits of annual FIT versus ten-yearly colonoscopy screening at differing ADR levels (quintiles; averages 15.3–38.7%), with colonoscopy performance assumptions estimated from community-based data on physician ADRs and patients’ post-colonoscopy risk of cancer. For patients receiving FIT screening with follow-up colonoscopy by physicians from the highest ADR quintile, simulated lifetime cancer incidence and mortality were 28.8 and 5.4 per 1000, respectively, versus 20.6 and 4.4 for primary colonoscopy screening (risk ratios, RR=1.40; 95% probability interval (PI), 1.19–1.71 for incidence, and RR=1.22; 95%PI, 1.02–1.54 for mortality). With every 5% point ADR decrease, lifetime cancer incidence was predicted to increase on average 9.0% for FIT versus 12.3% for colonoscopy, and mortality increased 9.9% versus 13.3%. In ADR quintile 1, simulated mortality was lower for FIT than colonoscopy screening (10.1 versus 11.8; RR=0.85; 95%PI, 0.83–0.90), while incidences were more similar. This suggests that relative cancer incidence and mortality reductions for FIT versus colonoscopy screening may differ by ADR, with fewer predicted deaths with colonoscopy screening in higher ADR settings and fewer deaths with annual FIT screening in lower ADR settings.