Several HSO3-functionalized halloysite nanotubes (HSO3-HNTs) were prepared by different methodologies including one-pot organosilylation or sulfonation and two-step organosilylation followed by sulfonation or oxidation. Their physicochemical characterization confirmed the success of HSO3-functionalization with S contents and acidity up to 1.61 mmol S/g and 3.67 mmol H+/g. All HSO3-HNTs were tested as acid catalysts in the esterification of free fatty acids (FFAs) mixture as hybrid feedstock model. Materials obtained from one-pot organosilylation or sulfonation and from two-steps involving sulfonation were the most active showing almost 100% conversion after 3 h: the one obtained by direct sulfonation exhibited the highest TOF (94 h(-1)) and mass normalized activity (0.08 mol g(-1) h(-1)), whereas that obtained by one-pot organosilylation showed the highest stability and reusability. The increase of FFA carbon chain length led higher conversions, showing the prevalence of inductive effect and absence of steric effects on the esterification mechanism using these new HSO3-HNTs catalysts.