Several studies have found the effect of cocoa bean fermentation on bioactive compounds through various fermentation characteristics; however, none of these studies adopted the meta-analysis approach. The effect of cocoa bean fermentation on six bioactive compounds: epicatechin, catechin, total phenolic content (TPC), anthocyanins, theobromine, and caffeine were systematically reviewed. This study aims to determine which variables that can affect the loss of bioactive compounds during fermentation so that their decrease can be reduced. The Cochrane Library, Medline, Science Direct, and Google Scholar databases were used to search the literature through November 2021. Twenty-nine studies were systematically reviewed, and 15 of them could be processed for meta-analysis. The results of the random effect model (REM) showed that cocoa bean fermentation significantly (p < 0.05) reduced the levels of catechins, epicatechins, TPC, anthocyanins, theobromine, and caffeine. The results of the study explain the concept that fermentation can reduce the number of bioactive compounds in cocoa beans. However, with certain genotype varieties, pod storage treatment and the addition of starter cultures are considered to be able to maintain a certain concentration of bioactive compounds.