The recovery of ecosystem processes in severely disturbed systems is often limited by biological resources in the soil. The objective of this study was to direct soil microbial biomass (SMB) size and activity with organic amendments. These amendments were applied to the soil at different amendment locations (incorporated versus surface-applied) and amounts (none, light, and heavy) in a 2 × 3 factorial design. The size and activity of SMB, soil nutrients, and aboveground biomass were monitored over 3 years to determine the rate and direction of change. Contrary to expectations that SMB and carbon mineralization potential (C-MIN) would be larger with amendment incorporation, SMB-carbon was greatest in the surface-heavy treatment and lowest in the incorporated-control treatment. SMB-nitrogen, C-MIN, and organic carbon were greater in the surface than in the incorporated treatments and in amended plots compared to controls. This departure from expectations suggests that other factors, such as microclimate or vegetation, are interacting with the amendment to affect SMB. The degree of contribution, however, is unclear. The treatments only affected planted aboveground biomass early in the experiment, with greater total biomass in the surface-light treatment in fall 2003. There was also a significant positive relationship between aboveground biomass and SMB in fall 2004. Inorganic nitrogen, total nitrogen, and the soil quality indicators qCO2 and Cmic/Corg did not vary systematically with amendment treatment. In general, amendment addition did enhance soil biotic properties and supported increased vegetation, but the complication of incorporating the amendment was not necessary for promoting biological development in disturbed soils.