Many metals are toxic in human organism, as is the case of cadmium and lead. Therefore, the metal levels in food need to be controlled. In coffee, metals may present risks when they are extracted from the powder to be consumed as beverage. A flow injection analysis (FIA) system is proposed, with atomic absorption detection, to metal adsorption studies in coffee powder. Kinetic study, best isotherms and time, and mass influences were determined. They allowed analyzing the high lead and cadmium adsorption percentage in organic and conventional ground coffee. Metal adsorption occurs in multilayers, following Freundlich’s model, and the kinetic model obeyed is the pseudo-second order. The cadmium adsorption suffered higher temperature influence, while the lead retention suffered higher mass influence. This study indicates that the majority of these toxic agents will be retained in the powder and will not be consumed by man, avoiding possible deleterious effects.