The cultivation systems of Coffea spp. in a cooperative society in Puebla, Mexico, include Rustic, Traditional Polyculture, Commercial Polyculture, Unshaded Monoculture and Shaded Monoculture. In this work, the properties of the soil were analyzed through physical, chemical and biological analyses to determine its nutritional status. Composite sample analyses were conducted to determine physical, chemical and microbiological parameters (fungi, actinomycetes, mesophilic bacteria, nitrifying and denitrifying bacteria). Leaf nutrients were determined. Rustic was the cropping system with the highest amount of K in the soil and nutrient assimilation in the leaf (N, P, K and Fe) (p = 0.001); in addition, it had high populations of mesophilic bacteria, fungi and actinomycetes and very low nitrification and denitrification rates. The principal component analyses (PCA) (>3.25%) indicated that actinomycetes and K in soil favor the assimilation of Fe, K and P. This Coffea spp. cultivation system generated a lower impact on soil health than the rest of the systems and favored forest ecosystem conservation.