Resistant starch (RS) has gained interesting because of its health benefits as the control of diseases, such as diabetes. Modifications in starches have been applied in order to increase RS content and consequently the range of industrial food applications. The heat-moisture treatment (HMT) combined with the addition of organic acids was the aim of this study, and also to evaluate the in vitro digestibility and other properties of corn starches. In both botanical sources, the RS content increased significantly, for the normal type and the waxy. Among organic acids used, citric, followed by lactic and acetic acid, promoted the most evident alterations and showed promising results in the increasing of RS. The results obtained by this combined method open opportunities for further applications in functional foods as well as starch based encapsulation process.