This study aimed to evaluate the colonic fermentation profiles of both high-amylose and waxy maize starches in raw, cooked, and cooked-cooled forms, as measured by changes in short-chain fatty acid production and microbiota composition, using the Mucosal-Simulator of the Human Intestinal Microbial Ecosystem (SHIME). Adding starch (6 g/L) to basal feed promoted butyrate production in SHIME proximal and distal colon vessels. The cooked high-amylose starch induced the highest butyrate production in both colon vessels, while the cooked waxy starch induced the highest butyrate production in the distal but not the proximal colon vessel. All starch preparations increased Bifidobacteriaceae abundance in the proximal colon vessel (2- to 6-fold) and the Firmicutes/Bacteroidetes ratio. The cooked high-amylose starch increased Akkermansiaceae abundance in the distal (2-fold) but not the proximal colon vessel. The results indicate the cooking and cooling effect on starch fermentation outcome in successive colon regions depends on the starch amylose content.