Despite the recognized benefits of fecal occult blood test (FOBT) and mammography screenings, participation in breast (BC) and colorectal cancer (CRC) screening programs is still suboptimal. In this study we investigate municipal characteristics associated with their BC/CRC screening uptake profiles among women aged 55-69 years. Using data from 308 municipalities of Flanders during 2014–2017, a profile for each municipality based on its BC/CRC screening uptake compared with the median screening uptake was created. Logistic regression with generalized estimating equations was used to assess the associations between municipal characteristics and BC/CRC screening uptake profiles. The overall median uptake of cancer screening was higher for CRC (57.4%) than for BC (54.6%). The following municipal characteristics were associated with worse performance in terms of only CRC, only BC, or both CRC and BC screening uptake respectively: non-Belgian/Dutch nationality, diabetes, 65-69 age group; non-Belgian/Dutch nationality, diabetes, disabilities; GP attendance and having children; The following municipal characteristics were associated with better performance in terms of only CRC, only BC, or both CRC and BC screening uptake respectively: having a partner, undergoing preventive dental care, jobseeker rate, higher education, residential stability; having a partner, undergoing preventive dental care, jobseeker rate; average income and (early) retirement rate. This study’s results regarding the interrelation between the BC and CRC screening could be used to tailor interventions aimed at improving participation of the target population in both programs.