The unsustainable use of the soil of the deforested area at the Amazonian border is one of the greatest threats to the rainforest. Among the causes of land degradation in the humid tropics are phosphorus depletion (P), the decrease of soil organic matter (SOM) and the loss of basic cations. The aim of this study was determine the effects of different land uses on the dynamics of soil organic matter and phosphorus, to determine whether and how changes in the P and SOM can be used to assess the degree of land degradation in the humid tropics and whether the use of ecological systems can lessen or mitigate this degradation. Five systems were chosen according to potential use in the region: pasture of 30 years; no-tillage with 5 years of rice–maize rotations; no-tillage in alley cropping systems of 10 years; a newly cleared area; and 20 years of undisturbed secondary forest. Each field was sampled in a “W” pattern, to collect the soil samples from the chosen systems, prior to the chemical analyses. The SOM was separated by physical soil fractionation. The soil P fractionation was performed. All of the soil samples showed a very low pH range. The potential acidity was high under the alley cropping system, with more intensive and continuous use. All of the more labile fractions of organic matter decreased with the continuous use of soil in the alley cropping system. Therefore under alley cropping, most of the P (approximately 95%) was found in an inorganic form, and approximately 60% was found in the less labile fractions. The pasture and secondary forest showed higher contents of the labile fractions of organic matter and organic P. Higher correlations of organic P were found with the silt and clay fractions of organic matter. The results indicate that the fractions of P and organic matter are important indicators to assess changes in the degree of land degradation in the humid tropics. These results indicate also that the intensive and continuous use of annual crops in the soils of the humid tropics must be considered as posing a high risk to the sustainability of the agrosystems, mainly because of the increase of the active and potential acidity, the decrease of the labile organic matter and the depletion of the pools of organic P, leading to land degradation.