Numerous studies have reported health benefits associated with the consumption of fresh and black garlic, which are characterized by the presence of polyphenols and organosulfur compounds (OS). This study aims to analyze the bioaccessibility of the bioactive compounds in fresh and black garlic after in vitro gastrointestinal digestion by monitoring the individual profile of these compounds by ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS). Polyphenols decreased from the beginning of the digestive process, is mainly affected during intestinal digestion. Regarding the OS, the S-alk(en)yl-L-cysteine (SACs) derivatives were more influenced by the acidic conditions of the gastric digestion, while the γ-glutamyl-S-alk(en)yl-L-cysteine (GSAk) derivatives were more susceptible to intestinal digestion conditions in both the fresh and black garlic samples. In conclusion, after in vitro gastrointestinal digestion, the compounds with the highest bioaccessibility were vanillic acid (69%), caffeic acid (52%), γ−glutamyl-S-methyl-L-cysteine sulfoxide (GSMCS) (77%), and S-allylmercapto-L-cysteine (SAMC) (329%) in fresh garlic. Meanwhile, in black garlic, the main bioaccessible compounds were caffeic acid (65%), GSMCS (89%), methionine sulfoxide (262%), trans-S-(1-propenyl)-L-cysteine (151%), and SAMC (106%). The treatment (heating + humidity) to obtain black garlic exerted a positive effect on the bioaccessibility of OS compounds, 55.3% of them remaining available in black garlic, but only 15% in fresh garlic. Polyphenols showed different behavior regarding bioaccessibility.