Coffee is one of the most important agricultural products in international trade. The agricultural management system may influence the chemical composition of the beans in addition to altering the bioavailability of nutrients essential for humans. Therefore, the concentrations of Cu, Fe, Zn and the proximate composition of powder and coffee infusions from beans grown under organic or conventional agricultural systems were evaluated. In addition, the effect of these products on hepatic mineral content in vivo was investigated, in healthy and induced cancer rats. Our results showed that the levels of Cu, Fe and Zn were higher in conventional coffee powder than in organic powder. However, despite these differences, the organic coffee had higher extraction yield for all infuses, and its infusion at 20% (w/v) had higher level of Zn than conventional infusion. These results were associated with the agricultural system used and the extraction process employed during the preparation of infusions. The conventional coffee provides more adsorbent compounds, decreasing the availability of this mineral in the beverage. In terms of the mineral content in vivo, the ingestion of diets prepared with infusions or coffee powder did not influence the hepatic content of Cu, Fe and Zn.