Metabolic syndrome (MetS) is a cluster of metabolic disorders primarily caused by central obesity, which results in chronic inflammation leading to hypertension, diabetes and atherogenic dyslipidemia. Inflammation underlying MetS could be the target for dietary flavonols as they present antioxidative properties. The aim of this paper was to analyze the differences in habitual intake of selected flavonols (quercetin, kaempferol, isorhamnetin and myricetin) between MetS patients and healthy participants, and its relationship with MetS advancement. Ninety participants were enrolled in this study. The one-year flavonol intake was assessed with a dedicated food frequency questionnaire. The patients with MetS consumed significantly less quercetin (p = 0.01), kaempferol (p = 0.04), isorhamnetin (p < 0.001), total flavonols (p = 0.01), tomatoes (p = 0.001) and wine (p = 0.01) daily. Further analysis revealed a moderate inverse correlation between quercetin (p = 0.001), kaempferol (p = 0.01), isorhamnetin (p < 0.001), total flavonols (p = 0.001) and tomato consumption (p = 0.004) and MetS stage. The analysis of laboratory parameters showed that dietary intake of flavonols was not correlated with lipid profile, glucose level or renal function. On the basis of this observation, a potential protective effect of dietary flavonols, mainly from tomatoes, against MetS could be suggested. However, when referring to MetS components, flavonols probably mainly impact central obesity and blood pressure, without a significant impact on conventional lipid-profile parameters and glucose level.