The article investigated the antioxidant and antimicrobial activity of extracts from two aromatic plants—Satureja hortensis L. (SE) and Rosmarinus officinalis L. (RE), encapsulated in alginate, on—yogurt properties. The encapsulation efficiency was controlled by FTIR and SEM analysis. In both extracts, the individual polyphenol content was determined by HPLC–DAD–ESI-MS. The total polyphenol content and the antioxidant activity were spectrophotometrically quantified. The antimicrobial properties of SE and RE against gram-positive bacteria (Bacillus cereus, Enterococcus faecalis, Staphylococcus aureus, Geobacillus stearothermophilus), gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Salmonella abony) and yeasts (Candida albicans) were analyzed in vitro. The encapsulated extracts were used to prepare the functional concentrated yogurt. It was established that the addition of 0.30–0.45% microencapsulated plant extracts caused the inhibition of the post-fermentation process, the improvement of the textural parameters of the yogurt during storage, thus the shelf life of the yogurt increased by seven days, compared to the yogurt simple. Mutual information analysis was applied to establish the correlation between the concentration of the encapsulated extracts on the sensory, physical-chemical, and textural characteristics of the yogurt.