Metabolic syndrome (MS) affects up to 40% of the population and is associated with heart failure, stroke and diabetes. Phytosterols (PS) could help to manage one or more MS criteria. The purpose of this study was to evaluate the therapeutic effect of daily supplementation of an aqueous dispersion of 2 g of free-phytosterols nanoparticles in individuals with MS over six months of intervention, compared with placebo. This double-blind study included 202 participants with MS randomly assigned into phytosterol (n = 102) and placebo (n = 100) groups. Participants were assessed at baseline, 4, 12 and 24 weeks. General health questions, anthropometric measurements and blood parameters were analysed. At week 24, the proportion of participants with high triglycerides (≥150 mg/dL) in the phytosterol group was 15.65% lower than in the placebo group (p-value = 0.023). Similarly, half of the participants in the phytosterol group decreased their waist circumference up to 4 cm compared with 0 cm in the placebo group (p-value = 0.0001). We reported no adverse effects (diarrhoea or vitamin D reduction); nonetheless, almost 70% of participants in the phytosterol group self-reported an improvement in bowel habits. Daily intake of free-PS nanoparticles improved some MS criteria; therefore, it might be a promising adjuvant therapy for individuals with MS (NCT02969720).