White and sweet potatoes can elicit different blood glucose responses depending on whether they are boiled or baked. This work investigated how microstructure and starch digestion in vitro relate to these differences. The main methods were INFOGEST's semi-dynamic digestion protocol, Scanning Electron Microscopy and Confocal Laser Scanning Microscopy. The cooking method impacted microstructure, thereby significantly influencing starch digestion. Boiling and baking led to similar types of microstructural changes, including cell expansion and separation and disruption to cell walls, with the differences lying on the magnitude of such changes. Hydrolysis of white potato starch into oligosaccharides during oro-gastric digestion stabilized at around 75% when boiled compared to 50% when baked. In sweet potato, hydrolysis during this stage represented 30% and 40% of the total starch after boiling or baking, respectively. Overall, the effect can be summarized as boiled white potato > baked white potato > baked sweet potato > boiled sweet potato. Our results show how structural transformations that occur during cooking can drive differences in starch release and hydrolysis during in vitro digestions. This work therefore provides a structural and biochemical basis to better understand the impact of boiling and baking on the glycemic responses to these foods.