This study was aimed at improving the functional attributes and shelf life of burrata cheese by using protective lactobacilli (Lactobacillus plantarum LPAL and Lactobacillus rhamnosus LRB), fructooligosaccharides, and inulin. Six burrata cheeses were made using (i) the traditional protocol (control), (ii) the addition of 0.5% fructooligosaccharides and inulin (DF cheese), (iii) protective lactobacilli in milk alone (PL cheese), (iv) protective lactobacilli in milk and governing liquid (2PL cheese), (v) protective lactobacilli in milk and dietary fibers (DF_PL cheese), and (vi) protective lactobacilli in milk and governing liquid and dietary fibers (DF_2PL cheese). As expected, DF, DF_PL, and DF_2PL cheeses showed 1.5% of total fibers. Burrata cheeses produced by adding protective lactobacilli only in milk (PL and DF_PL cheeses) showed the lowest acidification during cheese making and storage. Lactic and acetic acids and ethanol were found at the lowest concentrations in these samples. Analyses of cultivable microbiota and the microbiome showed that protective lactobacilli reduced the house microbiota components (e.g., Streptococcus thermophilus, Lactococcus lactis, and Leuconostoc lactis) during cheese making and storage. Protective lactobacilli slowed the growth of staphylococci, coliforms, and Pseudomonas spp., especially in early storage. According to the different microbiome assemblies, burrata samples differed in peptide profiles and the levels of free amino acids. As shown by a sensory analysis, the addition of protective lactobacilli in milk improved the flavor and increased the shelf life of burrata cheese. In comparison to cheeses made using protective cultures only in milk, the shelf lives of those containing cultures also in the governing liquid were not further prolonged and they received lower acceptability scores by the panelists.IMPORTANCE This study provides more in-depth knowledge of the microbiome of burrata cheese and the set-up for a novel biotechnology using prebiotic dietary fibers and protective probiotic Lactobacillus plantarum LPAL and Lactobacillus rhamnosus LRB in milk. The biotechnology proposed in this study should be considered a useful tool to improve the functional value of burrata cheese. The use of protective lactobacilli in milk enhanced the flavor formation and shelf life of burrata cheese.