The antimicrobial and antioxidant effects of plant extracts are well known, but their use is limited because they affect the physicochemical and sensory characteristics of products. Encapsulation presents an option to limit or prevent these changes. The paper presents the composition of individual polyphenols (HPLC–DAD-ESI-MS) from basil (Ocimum basilicum L.) extracts (BE), and their antioxidant activity and inhibitory effects against strains of Staphylococcus aureus, Geobacillus stearothermophilus, Bacillus cereus, Candida albicans, Enterococcus faecalis, Escherichia coli, and Salmonella Abony. The BE was encapsulated in sodium alginate (Alg) using the drop technique. The encapsulation efficiency of microencapsulated basil extract (MBE) was 78.59 ± 0.01%. SEM and FTIR analyses demonstrated the morphological aspect of the microcapsules and the existence of weak physical interactions between the components. Sensory, physicochemical and textural properties of MBE-fortified cream cheese were evaluated over a 28-day storage time at 4 °C. In the optimal concentration range of 0.6–0.9% (w/w) MBE, we determined the inhibition of the post-fermentation process and the improvement in the degree of water retention. This led to the improvement of the textural parameters of the cream cheese, contributing to the extension of the shelf life of the product by 7 days.