Nasturtium (Tropaeolum majus L.) is a plant rich in bioactive compounds such as phenolic compounds, glucosinolates (GLS) and their hydrolyzed metabolites isothiocyanates (ITCs), which modulate signaling pathways related to lipid and carbohydrate metabolism. This randomized crossover trial explored the effect of intervention with a freeze-dried nasturtium drink on insulin response and lipid profile in prediabetic subjects. Ten (10) patients were randomly assigned to the following treatments: NT (nasturtium) and PLC (placebo) for 4 weeks and after this time the treatments were crossed for another 4 weeks. Biomarkers related to insulin resistance and lipid profile were measured at the beginning and the end of the intervention with each treatment. The consumption of 15 g NT (681 μmol of benzyl glucosinolate)/dose week for four (4) weeks resulted in a significant decrease in the concentration of LDL cholesterol (LDLc), Oxidized LDL (ox-LDL), Castelli's risk index I and II (TC/HDLc, and LDLc/HDLc) and Atherogenic Coefficient (non-HDLc)/HDLc). The results suggest that the nasturtium consumption might have a modulating effect on biomarkers related to cardiovascular disease, altered in subjects with chronic diseases, including type 2 diabetes. This study is the first in vivo study to explore the chronic effect of T. majus consumption in patients with prediabetes and shows the importance of continuing to explore this effect in studies with a larger number of participants.