Cacao (Theobroma cacao) trees are grown in tropical regions worldwide for chocolate production. We studied the effects of agroforestry management systems and cover cropping on soil microbial communities under cacao in two different replicated field experiments in Peru. In the first experiment, two agroforestry systems, Improved Traditional Agroforestry System (ITAS) and Improved Natural Agroforestry System (INAS), were compared. ITAS was a 'slash and burn’ system in which all native vegetation was removed prior to replanting with cacao and other trees while INAS used selective removal of uneconomical trees followed by cacao planting. Soil microbial communities were analyzed by phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Soils in the ITAS system had altered microbial community structure and a lower Gram-negative to Gram-positive ratio when compared to soils in the INAS system. However, soil microbial community structure was also affected by a large soil pH gradient (three pH units) across this experiment. In the cover crop experiment, five cover crops, Arachis pintoi (perennial peanut), Calopogonium mucunoides (calopo), Canavalia ensiformis (jackbean), Centrosema macrocarpum (centro), and Callisia repens (callisia), and two controls (one with and one without nitrogen fertilization), were compared. Cover cropping with centro or perennial peanut increased the Gram-negative to Gram-positive ratio, while centro reduced the fungal biomass. Microbial community structure was significantly affected by cover cropping. Our results indicate that management systems and cover cropping can affect soil microbial community structure in tropical agroforestry systems, but the effects of soil edaphic properties must be considered as well.