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Properly conducted cocoa fermentation is an important step for the production of high-quality chocolate. The aim of this work was to investigate the effect of four cocoa varieties (CCN51, PS1030, FA13, and CEPEC 2004) inoculated with Saccharomyces cerevisiae CA11 on microbial communities and the profile of volatile compounds and sensory characteristics of chocolate. The S. cerevisiae population increased significantly (p < 0.05) during the fermentations. The microbial communities varied according to cocoa variety fermentation as assessed by denaturing gradient gel electrophoresis (DGGE). The dominant yeasts were S. cerevisiae and Hanseniaspora guilliermondii, while Lactobacillus casei and Gluconobacter oxidans were the predominant bacteria in the four different fermentations analyzed. Sixty-one volatile compounds—including aldehydes (11), ketones (10), esters (14), acids (8), alcohols (8 …