The structural differences among amino acids influencing mineralization by soil minerals, and the role of phenols in this mineralization, is very important in C turnover and N and S transformations in soil. The objective of this study was thus to investigate the effect of birnessite and pyrogallol on the mineralization of amino acids. Using a specially designed reaction flask, amounts and distribution of CO2 and NH3 released were determined during 90-h reaction periods. The results show that birnessite enhanced the decarboxylation of amino acids. The amount of CO2 released with l-serine, l-phenylalanine, l-proline, dl-methionine, and l-cysteine without birnessite was not detectable, while with birnessite-amino acid, losses were 109 ± 0, 162 ± 3, 145 ± 2, 95 ± 2, and 182 ± 3 µmol, respectively. Since L-cysteine has the strongest reducing power among the amino acids examined, the amount of CO2 released with birnessite-l-cysteine was greatest. Birnessite enhanced the deamination of amino acids. The amounts of NH3 released with l-serine, l-phenylalanine, l-proline, dl-methionine, and l-cysteine without birnessite were not detectable, while those with birnessite-amino acid were 140 ± 4, 145 ± 5, 66 ± 6, 83 ± 2, and 226 ± 8 µmol, respectively. Birnessite enhanced the mineralization of methionine and cysteine to release SO2−4 in the supernatants of the reaction systems. The amounts of SO2−4 released with dl-methionine and l-cysteine without birnessite were 0.1 ± 0.0 and 0.2 ± 0.0 µmol, respectively, while those with birnessite-amino acid were 0.8 ± 0.0 and 112 ± 7 µmol, respectively. In conclusion, the enhancing effects of birnessite play an important role in C turnover and N and S transformations in soil.