We investigated factors associated with organised and non-organised colorectal cancer screening using faecal occult blood tests, based on data from 308 municipalities in Flanders (6.6 million residents, 57% of Belgium) during 2015–2017. Logistic regression with generalized estimating equations was used to assess the associations between municipal characteristics and organised and non-organised screening coverages. Factors associated negatively with both organised and non-organised screening: percentage of people aged 70–74 in the target population [OR (odds ratios) = 0.98, 95%CI (confidence interval): 0.97–0.99 and OR = 0.98, 95%CI: 0.96–0.999, respectively]; negatively with organised screening: average income [OR = 0.97, 95%CI: 0.96–0.98], percentage of people with a non-Belgian/Dutch nationality [OR = 0.962, 95%CI: 0.957–0.967]; positively with organised screening: percentages of men in the target population [OR = 1.13, 95%CI: 1.11–1.14], jobseekers [OR = 1.12, 95%CI: 1.09–1.15] and people with at least one general practitioner (GP) visit in the last year [OR = 1.04, 95%CI: 1.03–1.05]; positively with non-organised screening: number of patients per GP [OR = 1.021, 95%CI: 1.016–1.026], percentage of people with a global medical dossier handled by a preferred GP [OR = 1.025, 95%CI: 1.018–1.031]. This study helps to identify the hard-to-reach subpopulations in CRC screening, and highlights the important role of GPs in the process of promoting screening among non-participants and encouraging non-organised participants to switch to organised screening.