Consumption of organic food has grown much around the world in the last 20 years. Change in the profile of consumers who have increasingly sought a healthy diet is the major contributor to this phenomenon. In scientific literature, some studies have already shown the nutritional superiority of organic food in the individual evaluation of metabolites. However, few studies have assessed interaction among metabolites, especially the one between minerals and the food matrix. This information may have great relevance in determining the extractability of minerals, especially in food consumed through infusion, such as yerba mate, since this interaction can directly influence their solubility. Thus, this study aimed to use hot water extraction techniques (infusion and decoction) and the principal component analysis (PCA) to evaluate the differences between organic and conventional cultivation systems in absorption and availability of Ca, Mg, Fe, Mn, and Zn in yerba mate leaves and stems. The PCA showed that cultivation influences total mineral contents found in both leaves and stems. Results of extractability only showed differences in conventional leaf samples, from which all minerals under study were better extracted. Results point out a different interaction between minerals and the matrix, depending on the cultivation, and to the stronger interaction between the matrix and minerals in organic samples, a fact which leads to low availability of minerals for consumption.