Studies on longitudinal associations between diet quality and lipid and amino acid metabolism in children and adolescents are limited. We studied associations between diet quality and serum markers of lipid and amino acid metabolism in the Physical Activity and Nutrition in Children (PANIC) study. These analyses included 403 children aged 6–9 years at baseline, 360 re-examined 2 years later at age 9–11 years and 219 eight years later at age 15–17 years. Food intake was recorded over 4 days, and diet quality was assessed using the Finnish Children Healthy Eating Index (FCHEI). Fasting serum fatty acids, amino acids, apolipoproteins and lipoprotein particle sizes were analysed via NMR spectroscopy. Linear mixed-effects models, adjusted for sex, age, body fat percentage, pubertal stage and physical activity were used to analyse the associations. Better diet quality was linked to increased serum PUFA and reduced saturated and MUFA, alanine and VLDL particle size. Consuming more vegetables, fruits, berries, vegetable oils and margarine with at least 60 % fat, fish and whole grains is associated with higher serum PUFA, lower SFA and smaller VLDL particles. Conversely, consuming higher-fat dairy products and sugary products is associated with higher saturated and MUFA, branched-chain and aromatic amino acids and larger VLDL particles. A diet rich in fruits, vegetables, unsaturated fats and fibre, with reduced sugar consumption, promotes favourable metabolic changes relevant to cardiometabolic health.