Abstract Reliable assessment of soil functionality requires integrative indicators that capture biological, physicochemical, and environmental responses to land-use disturbances. This study evaluated whether a reduced suite of low-cost microbial, chemical, and microclimatic indicators is sufficient to discriminate soil functional states across agricultural fields, mining sites, and non-disturbed areas in Andisols of northeastern Antioquia, Colombia. Soil samples were analyzed for microbial abundance and respiration, organic carbon, moisture, solute concentration, and microclimatic variables. Dimensionality reduction and variable integration were performed using geometric means, factor analysis, and scoring functions. Three indicators: microbial respiration rate (MRRat/C), total dissolved solids (TDS), and relative air humidity (RAH), were identified as the most informative and least redundant within the multivariate domain. Factor analysis showed that microbial indicators contributed 34.77% of total variance, demonstrating their central role in distinguishing functional soil states. Soil Quality Indices (SQI) derived from nonlinear scoring functions with importance-coefficient weighting yielded the highest sensitivity in differentiating land uses, showing clear declines from non-perturbed to agricultural to mining areas. Results highlight the strong responsiveness of microbially mediated processes to disturbance and support the adoption of non-linear, weighted indices as early-warning tools for vulnerable tropical Andisols.