Four designed cocoa fermentations were conducted in separated wooden boxes with different strains inoculum. One was spontaneous fermentation with natural occurring microorganisms, another was inoculated with Saccharomyces cerevisiae, another was inoculated with Lactobacillus plantarum, and the other was inoculated with Acetobacter aceti. The experimental parameters, including the fermenting cocoa mass temperature, the pH value, the total acidity of the pulp and cotyledons of cocoa beans, along with the fermentation time were determined. Furthermore, the phenolic compounds (flavanols and procyanidins DP1-10) of chocolates were determined by normal phase HPLC. In addition, the rheological, textural properties, and color parameters of the chocolates were measured. Meanwhile, the electronic nose was used to analyze the aroma compounds of the investigated chocolates and the principal components analysis (PCA) was conducted to distinguish the flavor profiles among the chocolates. The consumer sensorial assessment was carried out to evaluate the organoleptic properties of chocolates and their overall acceptability. The quality of chocolates produced by the defined inoculum varied with each other with the exception of the FP and PAC content. Different inoculated fermentation methods affected the rheological, textural properties, and color parameters of the end product chocolates. Furthermore, they influenced the types and numbers of aroma compounds generated during fermentation. However, the impact is mainly on their levels of aroma compounds. From sensory point of view, chocolates produced from inoculated Acetobacter aceti BCRC12324 during fermentation had the highest score point of overall acceptability among the investigated chocolates. The high levels of 2-methylbutanal content occurred in this chocolate could be an adequate reply of this finding. The quality of chocolate from fermentation with Lactobacillus plantarum B0091 inoculum was similar to the others, but some properties such as rheological, textural, and flavor profiles were inferior and less pronounced, leading to a slightly poorer response by the sensory panel. PCA successfully discriminates the aroma profiles into four groups, providing a better visualization of the variation among the chocolates produced by the different strains. This attempt to manipulate the strains during cocoa fermentation is a new approach in Taiwan chocolate industry. By controlling the starter culture of fermentation properly, we could improve the quality and flavor profiles of chocolate with a consistent and more reliable production.