Flavonoids are a key class of polyphenols, i.e., phytochemical compounds present in foods and beverages, which have been described as having health benefits in preventing several chronic diseases. Estimating flavonoid intake has already been conducted in several countries but has yet to be performed in Portugal. This study included 5,005 participants aged 3-84 years and aimed to estimate dietary flavonoid intake in the Portuguese population, using data from the National Food and Physical Activity Survey 2015-2016, providing information on intake, main food contributors, and the socio-demographic factors associated with the intake. Food intake data from the Survey was converted to flavonoid intake using a database built to include the most updated USDA databases on flavonoids, isoflavones and proanthocyanidins, and the Phenol-Explorer database. The rationale for combining food consumption data and different flavonoid databases using the FoodEx2 classification system was established. Linear regressions assessed the associations between socio-demographic factors and dietary flavonoid intake. The total flavonoid intake of the Portuguese population was estimated to be 107.3 mg/day. Flavanols were the most representative subclass, followed by flavonols, anthocyanidins, flavanones, flavones and isoflavones. Fruits and vegetables were the primary food contributors, providing 31.5% and 12.4% of the total flavonoid intake. Adolescents had the lowest total flavonoid intake, and older adults had the highest. This study provides information on the Portuguese population’s dietary flavonoids, allowing for international comparisons. It can also streamline forthcoming investigations into the link between flavonoid consumption and its impact on health, contributing to the future establishment of dietary reference values.