Cocoa is traditionally grown in agroforestry systems (AFS). It is essential to the household and regional economy and plays an important role in natural resource and environmental services conservation. In recent years, the vegetation structure and diversity of cocoa AFS throughout the world are being simplified as farmers consider that the removal of trees helps to increase yields and reduce disease incidence. However, debate exists on the relationship between tree shade and diversity and cocoa yields and the incidence of disease such as frosty pod rot, one of the most important fungal infections in cocoa cultivation. The objective of this study was to analyze changes in agroforestry structure, plant species diversity, uses, yields, the incidence of frosty pod rot disease in cocoa agroforestry systems, and discuss the consequences of the simplification of this particular AFS in the municipality of Acacoyagua, Chiapas, Mexico. Inventories were carried out in 27 plots. Interviews were applied to families to assess ecological, technical, and productive variables. Incidence of frosty pod rot disease and yields were estimated on-farm and through interviews over a period of 3 years. Multivariate cluster analysis, Pearson correlation analysis, the Levene test for equality of variances and a non-parametric U Mann–Whitney test were carried out. Three types of cocoa agroforests were identified as a result of a structure simplification: (1) traditional cocoa polyculture; (2) cocoa with Legumes Inga spp and Lonchocarpus spp.; and (3) cocoa with diverse, scattered, predominantly wild trees. Fifty species were recorded in shade vegetation, with a diversity index of 3.15. Simplification in tree structure did not have a significant effect on cocoa yield nor on the incidence of frosty pod rot disease. On the contrary, it resulted in a decrease in plant diversity and provisioning of food and other products. Farmers undertake few agricultural practices; some practices are eventually carried out, such as the pruning of cocoa trees and shade-trees, removal, and burial of diseased fruits, and weeding. Seven out of 27 plots sampled yielded more than 300 kg ha−1, and one plot attained a yield of 437.5 kg ha−1; however, yields averaged 155.8 kg ha−1 and incidence of frosty pot rot averaged 9.6%, regardless of AFS type. These results highlight the importance of improving AFS management which in this case appears to be the most critical factor for attaining an increase in yields. Low levels of production and the incidence of frosty pod rot subsequently reduces farmers’ motivation to continue cultivating cocoa, placing the crop at risk and increasing the possibility of a change in the land-use.