Bee‐pollen is a product collected by bees, gathered for human consumption given its nutritional and bioactive characteristics. However, its external structure is extremely recalcitrant and prevents nutrients and bioactive compounds to be completely digested into the gastrointestinal tract. The aim of this study was to assess enzymatic hydrolysis as a strategy to modify the structure of bee‐pollen and promote the release of compounds. Six different commercial enzymes were used and treatments were evaluated by Differential Scanning Calorimetry and Scanning Electron Microscopy, as well as protein, amino acids, phenolics, flavonoids, and antioxidant activity. The calorimetric analysis showed an increase in the heat flow of hydrolyzed products compared to bee‐pollen. It was also found that proteases improved the protein content of about 13%–18%, phenolics 83%–106%, flavonoids 85%–96%, antioxidant activity up to 68%, and increased all essential amino acids. Finally, a total ranking method established as the best treatment hydrolysis with Protamex. Practical applications Bee‐pollen is an attractive food of plant origin from a nutritional and functional point of view. The modification of its structure through enzymatic hydrolysis increases the availability of compounds that theoretically could be assimilated more easily in the gastrointestinal tract, improving the quality of bee‐pollen as a food resource. The treatment is safe, relatively inexpensive and easy to apply, compared to other bee‐pollen modification strategies such as fermentation.