Recently, there has been a renewed interest in the fermentation of kefir grains using fruit-based substrates, such as coconut water. Kefir grains contain a mixture of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeast, which have important probiotic capacity and play a vital role in improving the nutritional and functional properties of the new product being developed. The principal objective of this study was to determine the functional properties of the microorganisms identified and characterized from kefir, CWK, and sourdough fermented with coconut water kefir (CWKS), such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, L. fusant, L. reuteri, L. kunkeei, Acetobacter aceti, A. lovaniensis, A. pasteurianus, Candida kefyr, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, C. guilliermondii, and C. colliculosa. In addition to identifying functional properties, such as glutamic acid production, phytase production, phytic acid degradation, and exopolysaccharide production, from this study, it was found that significantly high quantities of glutamic acid, exopolysaccharide, and phytase enzyme were detected in two LAB isolates, Limosilactobacillus fermentum and Lactiplantibacillus plantarum.