The PICT method (pollution-induced community tolerance) can be used to assess whether changes in soil microbial response are due to heavy metal toxicity or not. Microbial community tolerance baseline levels can, however, also change due to variations in soil physicochemical properties. Thirty soil samples (0–20 cm), with geochemical baseline concentrations (GBCs) of heavy metals and from five different parent materials (granite, limestone, schist, amphibolite, and serpentine), were used to estimate baseline levels of bacterial community tolerance to Cr, Ni, Pb, and Zn using the leucine incorporation method. General equations (n = 30) were determined by multiple linear regression using general soil properties and parent material as binary variables, explaining 38% of the variance in log IC50 (concentration that inhibits 50% of bacterial growth) values for Zn, with 36% for Pb, 44% for Cr, and 68% for Ni. The use of individual equations for each parent material increased the explained variance for all heavy metals, but the presence of a low number of samples (n = 6) lead to low robustness. Generally, clay content and dissolved organic C (DOC) were the main variables explaining bacterial community tolerance for the tested heavy metals. Our results suggest that these equations may permit applying the PICT method with Zn and Pb when there are no reference soils, while more data are needed before using this concept for Ni and Cr.