Brazil has always been one of the most important coffee producing countries. Lately, there has equally been a renewed interest in alternative coffee production systems. The state of Espírito Santo is the second greatest coffee producer in Brazil; so, we used local coffee plantations to evaluate the relations between soil macrofauna and chemical and microbiological soil properties to identify which of these properties discriminate more effectively between the organic management system (OS) and the conventional management system (CS) of coffee plantations. For each of these two cultivation systems we chose three coffee farms who employed both cultivation systems and picked out the most similar fields from each property. At each site, first we sampled the litter at the soil surface. Afterwards, we sampled nine soil monoliths to evaluate the macrofauna, in summer and winter. We also collected nine supplemental soil samples, taken at a few centimeters from the soil monoliths, for chemical and microbiological analyses. Macrofauna density was evaluated by ANOVA and multivariate analysis. The chemical and microbiological properties are environmental variables, while the data on macrofauna are the explanatory variables. The total number of individuals recovered in this study was 3,354, and the climate, identified by the sampling season, was a great modulator of macrofauna, with higher numbers in winter. The principal components analysis showed that soil moisture, organic matter, nitrogen, phosphorus, boron, copper, pH, acid and alkaline phosphatases and microbial biomass carbon, were the most outstanding ones to discriminate both cultivation systems. We found no statistical significant differences in macrofauna density between OS and CS, probably due to a general great variability, since there was a tendency for much greater values in OS. We detected the interference of chemical and microbiological soil properties on the macrofauna community in both systems of coffee cultivation, and some results clearly correlated much better with climate data than with other factors. To our knowledge, this is the first time in which the data point to a clear separation between the more numerous and diversified soil macrofauna in coffee with organic cultivation from that with a conventional cultivation system.