A landfill was removed on the Presidio of San Francisco in 2003 exposing 2.2 acres of native soil derived from the Colma Formation. Twenty-four replicated 3 x 3 m plots were distributed across the site and planted in summer 2003. Six common native species with broad environmental tolerances were used. Two additional Non-Planted Control Plots were established on site. Two Reference Sites were sampled from nearby sites on a similar substrate with a remnant plant community. Soil samples were collected from each of the plots and reference sites and analyzed for a broad range of soil organisms. After one year Planted Plots exhibited lower diversity than Reference Sites for all soil microorganisms (anaerobic bacteria, 0.2 vs. 1.1; yeasts and molds, 0.3 vs. 0.9; Actinomyctes, 0.0 vs. 0.4; Pseudomonads, 0.8 vs. 1.2; N-fixing bacteria, -0.1 vs. 0.7; percent of roots colonized by mycorrhizae 4.0% vs. 32.5%) except Aerobic bacteria (1.9 vs. 1.8). After three years every previously low soil biological measure has increased and approaches reference conditions. Plant growth has been slower than expected but plant survivorship remains high (78%). After one year Control plots had soil organism diversity similar to planted plots but supported few total soil organisms. After three years control plots had changed little in diversity but the number of soil organisms increased. Overall Control Plots soil conditions improved more slowly than planted plot conditions.