The association between modifiable risk factors and caries in children has been documented; however, most studies have been cross-sectional and have not considered the complexity of dietary factors and oral health habits. This study aimed to investigate the prospective association between dietary patterns and oral health behaviours at 4 years of age and the development of new decayed, missing, and filled teeth (d3–6mft/D3–6MFT) over a period of three years. Participants were children from the Generation XXI population-based birth cohort. At 4 years of age, diet patterns were assessed using a food frequency questionnaire, with three dietary patterns being identified. For the purpose of capturing the new development of caries between 4 and 7 years of age, two dental outcomes were defined in the mixed dentition: “dental caries development” and “severe dental caries development” in the mixed dentition. Bivariate analysis and multivariate logistic regression were used. From 4 to 7 years of age, 51.2% of the children had at least one new d3–6mft/D3–6MFT and 27.4% had more than two new d3–6mft/D3–6MFT. Children belonging to the “energy-dense foods” (OR = 2.19; 95% CI: 1.20–4.00) and “snacking” (OR = 2.19; 95% CI: 1.41–3.41) dietary patterns at 4 years old were associated with severe dental caries development three years later. Preventive strategies should be implemented in an attempt to reduce snacking and the consumption of energy-dense, micronutrient-poor foods to promote children’s oral health.