Soils developed on relict hydrothermally altered soils throughout the Western USA present unique opportunities to study the role of geology on above and belowground biotic activity and composition. Soil and vegetation samples were taken at three unaltered andesite and three hydrothermally altered (acid-sulfate) sites located in and around Lassen VolcanicNational Park in northeastern California. In addition, three different types of disturbed areas (clearcut, thinned, and pipeline) were sampled in acid-sulfate altered sites. Soils were sampled (0–15 cm) in mid-summer 2010 from both under-canopy and between-canopy areas within each of the sites. Soils were analyzed for numerous physical and chemical properties along with soil enzyme assays, C and N mineralization potential, microbial biomass-C and C-substrate utilization. Field vegetation measurements consisted of canopy cover by life form (tree, shrub, forb, and grass), tree and shrub density, and above-ground net primary productivity of the understory. Overall, parameters at the clearcut sites were more similar to the unaltered sites, while parameters at the thinned and pipeline sites were more similar to the altered sites. We employed principal components analysis (PCA) to develop two soil quality indices (SQI) to help quantify the differences among the sites: one based on the correlation between soil parameters and canopy cover, and the second based on six sub-indices. Soil quality indices developed in these systems could provide a means for monitoring and identifying key relations between the vegetation, soils, and microorganisms.