The methods used to estimate the bioavailability of elements have different approaches. These tests are based on selective extraction or simulation of the physiology of the gastrointestinal tract. The sample preparation methods require studies about extraction procedures, thermal treatment, and decomposition of organic matter. The method of decomposing organic matter assisted by microwaves introduced adequate results for most chemical elements in pulses. The content of the elements present in the extracts obtained by employing the method physiologically based extraction test (PBET) is lower than those obtained by simple bioaccessibility extraction test (SBET) due to complexing effects of metal ions. The mineral content in the gastric and intestinal stages can vary significantly with the investigated leguminous species and the elements. The thermal processing can affect the concentrations of the elements analyzed in samples from leguminous species. This results from the heat capacity to change the speciation of chemical elements. The change speciation may modify the solubility and mobility of chemical species under the conditions of the gastrointestinal tract, which alters the bioavailability. In this sense, it can be concluded that the domestic cooking process can influence the nutritional and toxicological potential of pigeon pea, cowpea, and mangalo.