The adaptive character of soil microbial communities to metal pollution allows discriminating soil health, since changes in microbial populations and activities may function as excellent indicators of soil metal pollution. Volcanic soils are unique naturally fertile resources, extensively used for agricultural purposes and with particular physicochemical properties that may result in possible accumulation of toxic substances, such as trace metals. The aim of this study is to assess functional diversity of soil microbial communities in volcanic soils under different agricultural land use practices (conventional, traditional and organic), based on a three-tier approach: Tier 1 – assess soil microbial activities [microbial biomass carbon, basal soil respiration, metabolic quotient, enzymatic activities (β-glucosidase, acid phosphatase and dehydrogenase) and RNA to DNA ratio), Tier 2 – link the microbial activity to soil trace metal contamination and, Tier 3 – integrate the microbial activity in an effect-based soil index (Integrative Biological Response) to score soil health status in metal contaminated agricultural soils. Results showed that different agricultural practices in Andosols affected the soil microbial activities by decreasing the abundance of microbial biomass and enzyme activities of microorganisms involved in organic matter decomposition and nutrient cycling, regardless of soil microbial maintenance energy requirements (metabolic quotient) being similar to that of reference soils. The Integrative Biological Response values indicated that soil health was ranked as: organic (4.96) > traditional (12.94) > conventional (17.28) (the higher the value, the worse the soil health status), highlighting the importance of integrative biomarker-based strategies for the development of the trace metal “footprint” in Andosols. The observed pattern of soil microbial responses reflects the disturbance and stress that agricultural practices cause, as a result of the progressive accumulation of trace metals in soil matrix and the decrease of soil organic matter quantity and quality in the studied farming systems.