Humic acids (HAs) are redox-active components that play a crucial role in catalyzing relevant redox reactions in various ecosystems. However, it is unclear what role the different compost-derived Has play in the dissimilatory Fe(III) bioreduction and which chemical structures could accelerate Fe reduction. In this study, we compared the effect of eighteen HAs from the mesophilic phase, thermophilic phase and mature phase of protein-, lignocellulose- and lignin-rich composting on catalyzing the bioreduction of Fe(III)-citrate by Shewanella oneidensis MR-1 in temporarily anoxic laboratory systems. The chemical composition and structure of different compost-derived HAs were analyzed by UV–Vis spectroscopy, excitation-emission matrices of the fluorescence spectra, and 13C-NMR. The results showed that HAs from lignocellulose- and lignin-rich composting, especially in the thermophilic phase, promoted the bioreduction of Fe(III). They also showed that HA from protein-rich materials suppressed significantly the Fe(II) production, which was mainly affected by the amount and structures of functional groups (e.g., quinone groups) and humification degree of the HAs. This study can aid in searching sustainable HA-rich composts for wide-ranging applications to catalyze redox-mediated reactions of pollutants in soils.