Purified extracts from different types of berries and medicinal plants are increasingly used as raw materials for the production of nutraceuticals and dietary supplements, mainly due to their high content in bioactive substances. This is, for instance, the case of phenolic compounds such as flavonoids, which exhibit a wide range of beneficial properties, including antioxidant, anti-inflammatory, antineoplastic and antimicrobial activities. This paper tackles the characterization of several kinds of nutraceuticals based on hydrophilic interaction liquid chromatography (HILIC) with fluorescence detection (FLD). The study focused on the determination of flavanols and related compounds such as condensed tannins. Analytes were recovered by solvent extraction using methanol:water:hydrochloric acid (70:29:1 v:v:v) as the extraction solvent under sonication for 30 min at 55 °C. Experimental design with response surface methodology was used to optimize the HILIC separation to achieve good resolution of the main components, using acetonitrile:acetic acid (99:1 v/v) (solvent A) and methanol:water:acetic acid, (95:3:2 v/v/v) (solvent B) as the components of the mobile phase. For the assessment of the elution gradient, factors under study were solvent B percentage and gradient time. The best conditions were achieved with 10% solvent B as the initial percentage and 30 min of linear gradient to reach 25% solvent B. Principal component analysis and partial least square-discriminant analysis were used to characterize and compare the compositional features of dietary supplements based on both targeted and non-targeted approaches. Results revealed that the sample distribution relied on the oligomeric nature of descriptors.