Background The role of one-carbon metabolism and related B-vitamins in cognitive function in ageing is well-documented, particularly for folate and vitamin B12, with vitamin B6 and riboflavin receiving much less attention. ApoE is a well-established genetic risk factor for Alzheimer’s disease, but the role of B-vitamins in modifying this risk remains largely unexplored. We examined associations between folate, B12, B6, riboflavin, and cognitive function in older adults, including interactions with the ApoE ε4 genotype. Methods Community-dwelling older adults (≥ 60 years) from the Trinity-Ulster-Department of Agriculture (TUDA) study were stratified as ApoE ε4 carriers (ε3/ε4 and ε4/ε4 genotypes; n = 1205) or non-ε4 carriers (n = 3348). Cognitive function was assessed using the Repeatable Battery for Assessment of Neuropsychological Status (RBANS), the Frontal Assessment Battery, and the Mini-Mental State Examination. Logistic regression models were used to evaluate the association between cognitive dysfunction (defined as RBANS score < 80) and a range of variables, including biomarkers of folate, vitamins B12, B6, and riboflavin status, plasma homocysteine levels, and ApoE ε4 genotype. Results Lower status of vitamin B12 (holotranscobalamin; adjusted odds ratio (ORadj 1.30; 95% CI: 1.08–1.58, p = 0.007), vitamin B6 (ORadj 1.37; 95% CI: 1.12–1.67, p = 0.002), riboflavin (ORadj 1.73; 95% CI: 1.44–2.09, p < 0.001), and higher plasma homocysteine (ORadj 1.50; 95% CI: 1.22–1.83, p < 0.001) were each associated with higher risk of cognitive dysfunction. The ApoE ε4 genotype interacted adversely with low B12 status (p = 0.030) and elevated homocysteine (p = 0.008) in relation to cognitive outcomes. Conclusions Low status of vitamin B12, B6, riboflavin, and/or elevated homocysteine were each associated with a greater risk of cognitive dysfunction. A novel interaction between ApoE ε4 and low B12 or higher homocysteine was associated with an increased risk of cognitive dysfunction. Improving B-vitamin status may have important public health benefits for dementia prevention. Further investigation, ideally in the form of randomised trials, is however required to demonstrate a causative relationship and confirm whether intervention with B-vitamins can confer a beneficial effect in maintaining better cognitive health in at-risk older people. Trial registration TUDA study: https://bit.ly/4mYr1lx no. NCT02664584 (27/01/2016).