Chronic conditions such as obesity, inflammatory bowel disease (IBD), and colitis are associated with gastrointestinal (GI) inflammation and compromised GI barrier integrity. Cocoa may be a potential dietary strategy to mitigate gut-related conditions and been shown to elicit anti-inflammatory, antioxidant, and prebiotic effects. Alkali treatment of cocoa was once thought to reduce its bioactivity, but new evidence suggests it may enhance cocoa's health properties, through the formation of new, potentially bioactive high molecular weight compounds. Inulin, a fructose-containing plant polymer, exerts prebiotic effects and has also been investigated in the mitigation of IBD. This study aims to 1) investigate effects of alkali processing on gut health related bioactivity and phytochemical composition of cocoa and 2) evaluate potential additive benefits of combining cocoa and inulin. Polyphenolic and flavanol compounds in natural cocoa, alkalized cocoa, and inulin powders were characterized using Folin-Ciocalteu (total polyphenols) and 4-dimethylaminocinnamaldehyde (total flavanols) assays, thiolysis , and HILIC UPLC-MS/MS. Treatments of cocoa and inulin were made in 1:2 cocoa:inulin and 1:4 cocoa:inulin mixtures for both natural and alkalized cocoas. Cocoa mixtures, in addition to both cocoa powders and inulin alone, were subjected to an in-vitro digestion to generate material for an in-vitro fecal fermentation. Samples collected from the fermentation at 0, 6, 12, and 24 hours were analyzed via HPLC-MS for microbial metabolites, applied to HT-29 colon cancer cells to assess anti-inflammatory activity, and applied to a florescence assay measuring PLA2 inhibitory activity. The alkalized cocoa powder was found to have a significantly lower concentration of total polyphenols and total flavanols, as well as a lower mDP, suggesting that alkalization may affect larger procyanidins more than smaller flavanol compounds. Inulin enhanced the inhibition of the PLA2 enzyme and enhanced the IL-8 anti-inflammatory properties of cocoa, although the trends were weak. Overall, we did not see any clear, significant effects of alkalization or the addition of inulin to cocoa's colonic metabolite formation or its gut bioactivity in vitro. However, we have demonstrated that colonic fermentation of cocoa may have a negative effect on its bioactivity in vitro. Future research should further explore flavanol DP and bioactivity, fiber's interaction with polyphenols, colonic metabolism of cocoa, and cocoa's gut health effects in vivo. / Master of Science in Life Sciences / Gut conditions like obesity-associated inflammation and inflammatory bowel disease are highly prevalent, debilitating, and currently have no cure. Cocoa has been investigated as a possible dietary strategy for the mitigation and prevention of chronic inflammatory gut conditions due to its anti-inflammatory and enzyme inhibiting properties. Most attribute these effects of cocoa to its abundance of compounds called polyphenols. It is widely thought that the ability of cocoa to promote health is lost when cocoa beans are processed, because of the loss of polyphenols. Alkalization, or "Dutching", is an optional step in cocoa processing that some manufacturers perform to enhance flavor and color formation. Dutching cocoa can promote the polymerization of many smaller, flavanol, protein, and other compounds into larger, indigestible compounds. These indigestible compounds will not be absorbed in the small intestine and may be broken down in the large intestine by colonic bacteria, forming new metabolites. We obtained cocoa powders, one natural (not alkalized) and one alkalized and compared them in terms of content of polyphenols, bioactivities, and anti-inflammatory abilities. Additionally, we added a known prebiotic, inulin, to our cocoa formulations to determine if there are additive benefits of cocoa and inulin together. Ultimately, we found that alkalized cocoa contained lower concentrations of all polyphenolic compounds, even the larger compounds. Inulin enhanced the inhibition of digestive enzymes and the anti-inflammatory properties of cocoa, though not significantly. Inulin also reduced the pH (i.e. increased the acidity) of a simulated gut environment, which may be beneficial. Alkalization did not significantly affect cocoa's enzyme inhibitory activity or anti-inflammatory activity. Overall, the addition of inulin to cocoa does not seem to be effective in increasing cocoa's ability to treat and prevent gut diseases, but more information is needed.