The impact of different tropical farming systems on soil quality was examined using a systematic sampling strategy. Total organic C, pH, extractable P, exchangeable K, bulk density, water stable aggregates, microbial biomass C, cation exchange capacity, soil depth, and clay content were determined. An assessment framework, including a minimum data set, linear scoring functions and weighted additive indices, was used to evaluate the soil quality of a tropical farm growing various crops in Hainan, China. Soil quality was evaluated according to four functions: water availability, nutrient availability, rooting suitability, and erosion resistance. Our results showed that soils were intrinsically lacking in nutrients and vulnerable to degradation, and that these problems were exacerbated by inappropriate management. There was strong evidence that long-term rubber farming caused soil acidification, soil compaction, and depletion of organic matter and nutrients. By contrast, conservation practices in coffee plantations protected or improved organic matter concentration and soil structure, resulting in higher soil quality indices.