Background: Research on caffeine and cognitive performance remains controversial. Variations in genes associated with caffeine metabolism and response such as CYP1A2, AHR and ADORA2A may account for variable findings. Aim: To investigate caffeine × gene interactions on cognitive performance in all key domains of cognition in healthy individuals. Methods: Participants completed a lifestyle and food frequency questionnaire and a cognitive test battery including validated tasks to assess the domains of social cognition, memory, attention and executive function. Genotyping was performed for AHR rs6968554, CYP1A2 rs2472297, ADORA2A rs5751876, ADA rs73598374 and APOE rs429358 and rs7412. Results: Significant gene × caffeine interactions were observed for the domains of social cognition, ( F2, 123 = 5.848, p = 0.004) and executive function ( F2, 109 = 3.690, p = 0.028). ‘Slow’ metabolisers had a higher performance in social cognition compared with ‘fast’ metabolisers among high-caffeine consumers ( p = 0.004), while ‘fast’ metabolisers had a higher performance in executive function compared with ‘slow’ metabolisers among moderate caffeine consumers ( p = 0.002). Conclusions: The present findings suggest an association between genetic caffeine metabolism, habitual caffeine intake and cognitive function in the domains of social cognition and executive function. More research in naturalistic environments using larger cohorts is needed to confirm these findings to add to our understanding of how habitual caffeine may influence cognitive function based on individual genotype.