The objective of this work was to evaluate the soil macrofauna and the bioindicator taxonomic groups associated with different land uses in the Colombian Amazon. Twelve agroforestry arrangements were studied and compared with to the native forest and pasture. For each land use, six monoliths were randomly selected and divided into four layers (litter, and 0-10, 10-20, and 20-30 cm soil depths). The variables considered in the analysis of land use effects were: individuals per square meter, order richness, Shannon’s diversity index, and Pielou’s evenness index. The greatest values for soil macrofauna density and diversity occurred in the forest, in contrast with the pasture. The principal component analysis distinguished land use according to macrofauna diversity, separating the native forest from the other land uses. The cluster analysis indicated the potential of some agroforestry systems to conserve the values of soil macrofauna density and diversity similar to those of the forest. According to the analysis of indicator value, five taxonomic groups (Diplura, Pseudoscorpionida, Araneae, Chilopoda, and Gastropoda), identified as bioindicators, are associated with preserved sites because of the sensitivity of their populations.