Acacia caven (Mol.) Molina pollen causes pollinosis in South America. The aim of this work was to isolate, purify, and characterize the proteolytic enzymes of A. caven pollen, and study their influence on allergy. A series of chromatographic steps were applied to purify the proteolytic extract of A. caven pollen. The purified fraction was partially characterized, and then it was assayed on airway bioactive peptides (substance P, vasoactive intestinal peptide, and bradykinin), and peptide degradation was visualized by direct protein sequencing. The cellular detachment of an airway‐derived epithelial cell line (A‐549) was measured by methylene blue binding assay. The degradation of proteins from intercellular junctions (occludin, claudin, and E‐cadherin) was visualized by Western blot. A 75‐kDa peptidase, named acaciain peptidase, was purified and classified as a serine peptidase. Acaciain peptidase degraded bioactive peptides involved in the maintenance and recovery of the bronchomotor tone; it caused cellular detachment of A‐549 cell line, and degradation of intercellular junction proteins. Acaciain peptidase can alter the integrity of the epithelium barrier, causing cell permeability, increasing the allergic sensitization and exacerbating the overall bronchoconstrictive effect detected in asthmatic lungs. This novel serine peptidase constitutes a relevant therapeutic target in the treatment of allergic disorders.