We examined cross-sectional and longitudinal associations of dietary factors with caries experience in a population sample of 487 children aged 6–9 years at baseline examinations of the Physical Activity and Nutrition in Children (PANIC) Study. Altogether, 406 of these children attended 2-year follow-up examinations. Food consumption and eating frequency were assessed using 4-day food records, diet quality using the Baltic Sea Diet Score (BSDS), and eating behaviour using the Children’s Eating Behavior Questionnaire. Caries experience was examined clinically. The cross-sectional associations of dietary factors with caries experience at baseline were analysed using linear regression and the longitudinal associations of dietary factors with a change in caries experience over follow-up using generalised mixed-effects regression adjusted for other risk factors. Higher consumption of high-fibre grain products (standardised regression coefficient β = -0.16, p = 0.003), milk (β = -0.11, p = 0.025) and higher BSDS (β = -0.15, p = 0.007) were associated with lower caries experience, whereas higher consumption of potatoes (β = 0.11, p = 0.048) and emotional overeating (β = 0.12, p = 0.025) were associated with higher caries experience. Higher snacking frequency (fixed coefficient β = 0.07, p = 0.033), desire to drink (β = 0.10, p = 0.046), slowness in eating (β = 0.12, p = 0.027), and food fussiness (β = 0.12, p = 0.018) were associated with higher caries experience, whereas enjoyment of food (β = -0.12, p = 0.034) and higher BSDS (β = -0.02, p = 0.051) were associated with lower caries experience.