Eating problems are common among children with Autism Spectrum Disorder (ASD), but it is unknown to what extent infant eating behavior is associated with later autistic traits. As eating behavior is currently not included in ASD screening instruments, it is important to evaluate whether infant eating behavior predicts later autistic traits and might therefore be used to enhance the early detection of ASD. We investigated the association of breastfeeding and eating behavior during infancy with later autistic traits in the population-based Generation R cohort. We included 3546 mother-child dyads with maternal reports on feeding and eating at age two months and autistic traits at six years. Eating behavior was assessed with seven items on specific eating habits and the Social Responsiveness Scale was used to evaluate autistic traits. Covariates included child sex, and maternal psychopathology and autistic traits. Linear regression analyses showed that being formula fed at two months was associated with a higher autistic trait score at six years (adjusted B = 0.07; 95% CI: 0.00–0.14). Children who were drinking only small quantities (adjusted B = 0.17, 95% CI: 0.04–0.30) and were hungry/not satisfied (adjusted B = 0.23, 95% CI: 0.08–0.39) at age two months also had a higher autistic traits score at age six years. We found no interactions with sex or breastfeeding. This study shows that eating behavior during infancy is related with autistic traits in childhood. Although the associations were fairly small, these findings suggest that early-life eating problems might be relevant for early detection of ASD and a potential addition to ASD-specific screening instruments.