An extremely acid mine soil polluted with Cu was amended with pine bark, crushed mussel shell or a 1:1 mixture of these two by-products. The performance of the soil microbial community was measured as the bacterial and fungal community growth, which were monitored during 2 years following the amendments. Pine bark caused significant increases of microbial growth rates, but with distinct differences between fungal and bacterial groups. Bacterial growth increased transiently at intermediate rates of pine bark applications, but returned to control rates within 2 years of application. In contrast, pine bark applications consistently increased fungal growth with effects that were maintained throughout the study period. The addition of only crushed mussel shell to the mine soil caused very delayed positive effects on the bacterial growth and almost no significant effects on the fungal growth. However, the combination of pine bark with crushed mussel shells 1:1 mixtures caused positive growth responses of both bacteria and fungi that remained persistent throughout the 2 years of study. Fungal and bacterial growth were both suppressed in the mine soil by the lack of organic matter. In addition, bacterial growth was also secondarily suppressed by acidity, and hence, when organic matter (pine bark) additions were combined with pH increases (crushed mussel shell additions), bacterial growth was additionally stimulated. In conclusion, the proposed mixture of by-products (pine bark and crushed mussel shell) is suggested as a promising reclamation strategy for acid mine soils. These results also suggest that in soils like that studied here the organic matter limitation is a more important factor than the soil pH and Cu availability for fungal and bacterial performance.