Although prickly pear fruits have become an important part of the Canary diet, their native varieties are yet to be characterized in terms of betalains and phenolic compounds. To exert potential health benefits, these antioxidants must be released from the food matrix and be stable in the gastrointestinal tract. Our aim was to characterize the betalain and phenolic profile of four prickly pear varieties from the Canary Islands (Spain) and determine their digestive stability and bioaccessibility via in vitro gastrointestinal digestion. Digestive studies were performed considering the (i) importance of the edible fraction (pulps) and (ii) potential of fruit peels as by-products to obtain healthy ingredients. Betalains and phenolic profiles were analyzed by HPLC-DAD-ESI/MS and HPLC-DAD-MS/QTOF. Pulps in Colorada and Fresa varieties presented high indicaxanthin and betanin content, respectively. Despite low pH in the gastric phase, betalains were stable to reach the intestinal phase, although indicaxanthin presented a higher bioaccessibility. Blanco Buenavista peels contained a distinct flavonoid profile including a new isorhamnetin-hexosyl-rhamnoside. Phenolic compounds were abundant and highly bioaccessible in fruit peels. These findings suggest that prickly pear pulps are rich in bioaccessible betalains; and that their peels could be proposed as potential by-products to obtain sustainable healthy ingredients.