Non-communicable diseases such as gastric inflammatory diseases and the hepatic pathologies are mainly related to bad lifestyle habits such as recurrent consumption of non-steroidal anti-inflammatory drugs (NSAIDs), excessive intake of alcohol, tobacco, steroids (high doses), alkaline agents, strong acid foods, and high-fat food, and Helicobacter pylori infections, among others. The fruit of Opuntia oligacantha C.F. Först var. Ulapa (xoconostle) is currently being studied due its nutritional and functional properties. The objective of the present study was to evaluate gastroprotective, anti-inflammatory, and hepatoprotective activities of different parts of xoconostle fruit by establishing in vitro simulated gastrointestinal conditions. Four treatments were established to test aqueous extracts (pericarp (P), mesocarp (M), endocarp (E) and whole fruit (W)). The quantified bioactive compounds were the total phenols, flavonoids, tannins, and betalains. The enzymatic assays were: urease, elastase, and β-glucuronidase. Significant differences (p < 0.05) of bioactive compounds content were measured in xoconostle extracts, the highest concentration was found in W (phenols 313 mg GAE/100 g, flavonoids 189 mg QE/100 g, tannins 71 mg CATE/100 g). The betalains content was higher in E; 17 mg/100 g significant differences were observed (p < 0.05) in the enzymatic inhibitions test (urease, elastase and β-glucuronidase), where W presented the highest inhibition activity (86%, 79%, and 84%), respectively. Bioactive compounds after in vitro gastrointestinal tests were maintained above 60% enzymatic inhibition activity.