The characteristics of the soil in the Peninsula of Yucatán confer unique organoleptic properties to the habanero pepper (Capsicum chinense Jacq.), and thus this entity possesses the denomination of origin of the species, making these chilis the most coveted, nationally and internationally. However, the extreme microtopographic variation distinguishing the Peninsula complicates the transfer of technologies and the successful establishment of agricultural practices. Maya farmers of the region identify the brown soils as preferable for the cultivation of this chili, although there is some controversy among the farmers regarding the best yields when the quality of the water used for irrigation is poor. No studies of the effect of soil type on this plant have been carried out. This work evaluated the impact of three types of soil of the Peninsula (red, brown, and black) on growth, fruit production, and nutrient content in soils and plants, during different phenological stages. The results indicate that the red and brown soils were the best for the growth and production of the fruit. In the black soil, it was possible to observe greater retention and accumulation of sodium applied in the water used for irrigation and in the macronutrients N, P, K, which may have led to a negative effect in the development of the fruit in these plants. Moreover, the plants growing in red and brown soils seem to make a more efficient use of the nutrients, presenting higher values of N, P, and K in their tissues in the flowering-fructification stage. These results are particularly useful in the realization of agricultural plans with a lower consumption of fertilizers, which allows an increase in yield, particularly if we take into account the enormous problems of saline intrusion worldwide and in this region.