Consumers search for food with functional characteristics beyond its nutritional properties. Thus, the concept of functional food has become a hot topic, allowing us to obtain additional health benefits, including disease prevention. In this context, plants are recognized as sources of a wide range of bioactives, including phenolic compounds. Herein, rosemary aqueous extract was used as a functional ingredient for cottage cheese, after proving that it possesses both higher content of phenolic compounds and antioxidant activity, comparatively with the corresponding hydroethanolic extract. However, a decrease of bioactivity was observed for the cheese samples enriched with the extracts in free form after seven days under storage. Therefore, in order to preserve the antioxidant activity, the rosemary aqueous extract was efficiently microencapsulated by using an atomization/coagulation technique. Overall, the introduction of both free and microencapsulated extracts provided bioactivity that was better preserved with microencapsulated extracts without changing the nutritional value of cottage cheese.