In this study probiotic microcapsules with three different shell compositions were produced through enzymatic gelation of skim milk powder by rennet, skim milk powder by transglutaminase and sodium caseinate by transglutaminase. Fabricated microcapsules and free Lactobacillus paracasei cells were incorporated into Iranian UF Feta cheese with different salt levels. Viability of L. paracasei (LAFTI L26), antioxidative capacity, ripening index, titrable acidity, salt content and texture profile analysis (TPA test) parameters including hardness, cohesiveness and stringiness were monitored during 45 days of storage time. Rennet based encapsulation was the most efficient method and could keep L. paracasei viable in all cheese samples (> 7 log10 CFU/g) at the end of storage time. Proteolysis pattern and acidification rate were strongly influenced by shell composition, salt level and storage time. Hardness and stringiness of probiotic cheese samples were influenced by shell composition of microcapsules and storage time but cohesiveness was only dependent on storage time. Therefore, storage time was the only effective factor on free radical scavenging activity of cheese samples.