Ayocote beans (Phaseolus coccineus L.) are a rich source of some bioactive molecules, such as phenolic compounds that exhibit antioxidant capacity that promote health benefits. Ayocote is mainly consumed after cooking, which can impact the antioxidant characteristics of the phenolic compounds responsible for some of its health benefits. Therefore, this study investigated the effects of boiling on the phenolic composition and bioactivities of ayocote beans before and after boiling. Boiling decreased the total phenolic content (70.2, 60.3, and 58.2%), total anthocyanin (74.3, 80.6, and 85.7%), and antioxidant activity (DPPH: 41.2, 46.9, and 59.1%; ORAC: 48.23, 53.6 and 65.7%) of brown, black, and purple ayocote beans, respectively. All the extracts also inhibited the activity of α-glucosidase with efficacy values from 29.7 to 87.6% and α-amylase from 25.31 to 56.2%, with moderate antiglycation potential (15.2 to 73.2%). Phenolic acids, anthocyanins, and flavonoid decreases were detected in boiled samples by HPLC-MS analysis. Although boiling reduced the phenolic compounds, bioactive compounds remained in a considerable content in boiled ayocote.