Ponderosa pine forests play a significant role in regional soil organic carbon (SOC) budgets. However, the underlying mechanisms of SOC stabilization are poorly understood in these systems. We hypothesized that Al-humus complexes, short-range-order (SRO) Fe-oxyhydroxides, and soil acidity impact SOC stabilization and soil microbial community. We sampled a lithosequence of four parent materials (rhyolite, granite, basalt, limestone) under Pinus Ponderosa to capture a soil acidity gradient and to elucidate the effects of soil mineralogy and Al–chemistry on SOC dynamics and microbial community composition. Three soil profiles were examined on each parent material and analyzed by X-ray diffraction, total elemental analysis, CEC, pH, selective dissolution, C and N content, and 13C stable isotope signature. Microbial communities were examined by most probable number (MPN) analysis before and after treatment with varying concentrations of Al. In A horizons regression analysis indicated that SOC was only partially related to soil physical and mineral variables with significant positive correlations to clay content, Al-humus complexes and Al- substituted into free Fe-oxides. In subsurface B horizons, regression analysis indicated that Al-humus complexes (r² = 0.73; P = 0.0017) and short-range-order Fe-oxyhyrodixes (r² = 0.64; P = 0.0052) played a significant role in controlling SOC content. We also noted a shift in form of Al from predominantly monomeric, exchangeable forms in acid soils to Al-humus complexes in basic soils. Our results to date demonstrate variability in SOC stabilization mechanims between four parent materials and with depth, as well as pH and Al-controlled variability in microbial community.