The aim of this paper was to prepare a natural food additive based on the encapsulated aqueous extract of pot marigold flowers in the calcium alginate microparticles. The prepared extract had an antioxidants content of 5.59 g GAE/100 g of dry weight. Its antioxidant activity was expressed based on a half‐maximal inhibitory concentration which was found to be 0.096 mg/ml. The average particle sizes of control and encapsulated alginate microparticles prepared using extrusion‐assisted by a secondary airflow were 643.7 and 789.3 µm, respectively. The encapsulation efficiency of 87.4% was determined. The study has shown that the chemical interactions between bioactive compounds and alginate did not occur. The release of antioxidants from alginate microparticles was monitored in the conditions of the simulated gastrointestinal tract at 37°C. The higher release of antioxidants by about 70% was noticed in the simulated intestinal fluid. The application of alginate microparticles can ensure the safety of foodstuffs and increase their nutritional value in a way acceptable to the final consumers. Novelty Impact Statement Studies on the encapsulation of pot marigold flowers into the calcium alginate microparticles using extrusion‐assisted by a secondary airflow have important research value. The prepared system can be used as an additive of foodstuffs for the improvement of nutritional value and enhancement of their stability. The prolonged delivery system can enable the safe storage of products based on the long‐lasting release of antioxidants.