The aim of the study was to evaluate the influence of the red cabbage extracts on the bioaccessibility of their isothiocyanates, and their effect on the intestinal microbiota using a dynamic model of human digestion treated with the gut microbiome of obese adults. The elicitation of red cabbage plants with methyl jasmonate (MeJA) duplicated the content of glucosinolates (GSLs) in the plant organs used for elaborating the encapsulated formula. The use of plasma membrane vesicles, according to a proper methodology and technology, showed a high retention of sulforaphane (SFN) and indol-3-carbinol (I3C) over the course of the 14-day digestion study. The microbiome was scarcely affected by the treatments in terms of microbiota composition or the Bacteroidetes/Firmicutes ratio, but a 3 to 4-fold increase was observed in the production of butyric acid with the encapsulated extract treatment. Based on our pilot red cabbage extract study, the consumption of this extract, mainly encapsulated, may play a potential role in the management of obesity in adults.