Flavonoids are suggested to reduce disease risk. Since dietary habits are acquired during early life, describing age and time trends of flavonoid intake and major food sources are important for monitoring and disease prevention in later life. We aimed to describe total flavonoid intake and food sources and to investigate age and time trends of flavonoid intake in 3–18-year-olds, from the Dortmund Nutritional and Anthropometric Longitudinally Designed study from 1985 to 2016. Intake was assessed annually using 3-d weighed food records (WFR). Flavonoid values were assigned using the United States Department of Agriculture database. Foods contributing to intake were determined. Age and time trends in total flavonoid and isoflavone density were analysed by sex with PROC MIXED. In total, 1312 children completed 10 758 WFR. Across all ages, daily mean total flavonoid density was lower in boys compared with girls (134 v. 146 mg/4184 kJ) and no difference in median isoflavone density (0·04 mg/4184 kJ per d) was found. The top five foods contributing to total flavonoid intake were apple with peel (15·0/17·1 %), strawberries (5·9/6·1 %), chocolate spread (3·9/3·5 %), orange juice (3·5/3·4 %) and pasta (3·5/3·4 %) for boys and girls, respectively. Overall, in boys, total flavonoid density decreased over the course of age and time. In girls, there was no association with age or time. In both sexes, isoflavone density followed a U-shaped age trend with no change over time. From a public health perspective, the overall observed downwards trend of flavonoid intake in boys deserves attention. Future initiatives should be tailored at maintaining a high flavonoid density as children age, specifically among boys.