Black locust flower extract contains various polyphenols and their glucosides contribute to the potential health benefits. After intake of these bioactive compounds and passage through the gastrointestinal tract, their degradation can occur and lead to a loss of biological activity. To overcome this problem, the bioactive compounds should be protected from environmental conditions. This study aimed to encapsulate the black flower extract in the microparticles based on biodegradable polysaccharides, alginate, and chitosan. In the extract, the total antioxidant content was found to be 3.18 ± 0.01 g gallic acid equivalent per 100 g of dry weight. Also, the presence of lipids (16), phenolics (27), organic acids (4), L-aspartic acid derivative, questinol, gibberellic acid, sterol, and saponins (2) was confirmed using the UHPLC-ESI-MS analysis. In vitro assays showed that the extract has weak anti--glucosidase activity and moderate antioxidant and cytotoxic activity against the HeLa cell line. The extrusion method with secondary air flow enabled the preparation of microparticles (about 270 μm) encapsulated with extract. An encapsulation efficiency of over 92% was achieved in the alginate and alginate-chitosan microparticles. The swelling study confirmed a lower permeability of alginate-chitosan microparticles compared with alginate microparticles. For both types of microparticles, the release profile of antioxidants in the simulated gastrointestinal fluids at 37 °C followed the Korsmeyer-Peppas model. A lower diffusion coefficient than 0.5 indicated the simple Fick diffusion of antioxidants. The alginate-chitosan microparticles enabled a more sustained release of antioxidants from extract compared to the alginate microparticles. The obtained results indicated an improvement in the antioxidant activity of bioactive compounds from the extract and their protection from degradation in the simulated gastric conditions via encapsulation in the polymer matrixes. Alginate-chitosan showed slightly slower cumulative antioxidant release from microparticles and better antioxidant activity of the extract compared to the alginate system. According to these results, alginate-chitosan microparticles are more suitable for further application in the encapsulation of black locust flower extract. Also, the proposed polymer matrix as a drug delivery system is safe for human use due to its biodegradability and non-toxicity.