Land use change (LUC) has important effects on the aboveground biota, mainly by altering richness and diversity, as well as ecosystem functioning. However, the effects of LUC on abiotic and biotic soil properties need to be assessed to determine recovery potential when the original vegetation is restored. The Los Tuxtlas tropical rain forest landscape in Veracruz, Mexico, offers a suitable framework for testing this. To assess the effect of LUC on the microbial community of this tropical rain forest landscape, we analyzed the whole-cell fatty acid profile of the microbial community and physicochemical properties of soils from four types of land use: crops, pastures, secondary forest, and primary tropical rain forest for the dry and rainy seasons. Regardless of season, the microbial data grouped according to land use. The composition of the microbial community was correlated with soil pH in the dry season, and with nitrate, soil organic matter, and available phosphorus concentration in the rainy season. Land use affects the abundance of the microbial community as a function of seasonal variation. In comparison with the microbial community in primary and secondary forest, that of crops and pastures was more greatly affected by seasonal variation. In fact, there were no significant differences between the primary forests or among secondary forests of different ages. These results may indicate a capacity for fast recovery (5 years or less) by the microbial community upon forest regeneration.