Food parenting practices (FPPs) have an important role in shaping children’s dietary behaviors. This study aimed to investigate cross-sectional and longitudinal associations over a two-year follow-up between FPP and dietary intake and compliance with current recommendations in 6- to 11-year-old European children. A total of 2967 parent-child dyads from the Feel4Diabetes study, a randomized controlled trial of a school and community-based intervention, (50.4% girls and 93.5% mothers) were included. FPPs assessed were: (1) home food availability; (2) parental role modeling of fruit intake; (3) permissiveness; (4) using food as a reward. Children’s dietary intake was assessed through a parent-reported food frequency questionnaire. In regression analyses, the strongest cross-sectional associations were observed between home availability of 100% fruit juice and corresponding intake (β = 0.492 in girls and β = 0.506 in boys, p < 0.001), and between parental role modeling of fruit intake and children’s fruit intake (β = 0.431 in girls and β = 0.448 in boys, p < 0.001). In multilevel logistic regression models, results indicated that improvements in positive FPPs over time were mainly associated with higher odds of compliance with healthy food recommendations, whereas a decrease in negative FPP over time was associated with higher odds of complying with energy-dense/nutrient-poor food recommendations. Improving FPPs could be an effective way to improve children’s dietary intake.