Cocoa polyphenols and Lactobacillales have shown promising effects in mitigating the adverse health effects associated with high-fat diets by removing free fatty acids from the gastrointestinal tract. However, the successful incorporation of these bioactive agents into functional foods requires a protective mechanism capable of withstanding the challenging conditions encountered during processing, storage, and gastrointestinal transit. This study explores the microencapsulation parameters of fat-removing Lactobacillales strains, previously isolated from human intestinal microbiota, and cocoa polyphenols, and their performance during simulated digestion. The findings revealed that microencapsulated Lactobacillus sp. A1, the strain with the best encapsulation results, effectively removed fatty acids from the simulated intestinal fluid during in vitro digestion, and the presence of cocoa polyphenols had no detrimental impact on their fatty acid removal capacity. These results hold promise for the potential development of innovative functional foods for the prevention of health conditions associated with excessive consumption of fatty acids.