Polycondensation reactions between amino acids and phenols are one of the pathways for the formation of humic substances, and clay minerals are able to catalyse these reactions. To investigate the catalytic power of allophane, an allophane fraction (ALF) was separated from weathered pumice (WP) that contained imogolite as an impurity by taking advantage of differences in sedimentation velocity. The iron content in the separated ALF was increased by up to 3.0% compared to that in the starting WP (1.3%), and the ALF was further treated with sodium dithionate and citric acid (ALF-DC) to remove the iron. The catalytic powers of WP, ALF and ALF-DC were evaluated, based on the degree of darkening of reaction mixtures from polycondensation reactions between catechol and tryptophan, model compounds for precursors of humic substances. The catalytic power for ALF was significantly higher than the corresponding values for WP and ALF-DC. This can be attributed to the high iron content of the ALF, which serves as a Lewis acid that can enhance nucleophilic reactions which occur during the polycondensation reactions.