Bioactive peptides can be protected from the gastrointestinal environment by microencapsulation. The aim was to assess the effect of simulated gastrointestinal digestion on bioactive properties of P. lunatus peptides (ACE‐I, α‐glucosidase, α‐amylase, and dipeptidyl peptidase‐IV inhibition) microencapsulated by spray drying using maltodextrin/gun arabic in optimal formula. Microcapsules were formulated using a 22 factorial design. The simultaneous effect of P. lunatus hydrolysate (4 and 10 g 100 g−1) and proportion of maltodextrin/gum arabic (25:75 and 75:25 g 100 g−1) on yield, protein efficiency, size, protein release at pH 2.0 and pH 7.0 of the different microcapsules was studied. Microcapsules with maximum yield, protein efficiency, and protein release at pH 7.0, and minimum protein release at pH 2.0 were subjected to simulated gastrointestinal digestion. Microcapsules obtained in optimal formula preserved the α‐glucosidase, α‐amylase, and dipeptidyl peptidase‐IV inhibitory activity of P. lunatus peptides after in vitro gastrointestinal digestion.