We investigated the organic carbon pools and the microbial diversity and activity in anthropogenic terraced soils in a desert area of Southern Peru to highlight how the introduction of agriculture influences carbon evolution and storage and genetic and functional diversity of soil microbiota over time. Five sites were selected considering soils cultivated since 5, 15, 20, 35 and 65 years, sampled along the profile depth (0-20 and 20-40 cm layer). Soil and microbial parameters comprised by organic carbon pools, microbial respiration, microbial community physiological profile (CLPP) and microbial diversity (PCR-DGGE) were determined. The results showed that the highest C concentrations were reached after a long cultivation time (P65), at both depths. In this site Corg was mainly composed by chemically not extractable C, considered the most stabilized fraction. The remaining extractable C fraction decreased with the depth and was mainly made up of highly mineralizable compounds. Data showed that human transformations has affected organic carbon pools only after several decades of cultivation, whereas the activity and structure of the microbial community changed gradually over time, showing the major differences between the most ancient (65 years) and the most recent (5 years) anthropized soils.