Water kefir (WK) is a non-dairy microbial consortia composed by lactic acid bacteria (LAB), yeast and acetic acid bacteria (AAB) aggregates into a polysaccharide matrix. WK is generally cultivated in a sucrose solution, being considered as excellent source of probiotics. Fruits are the most diverse group that can be used for fermentation of WK grains. This work aimed to evaluate some microbiological and physicochemical characteristics, including the determination of biologically active substances (total phenolic compounds) and volatile organic compounds (VOCs) profile of kefir-like beverages obtained after fermentation of whole fruit juices (orange and grape) and coconut water. The fermentation process was carried out at 30°C for 24h using 125 mL Erlenmeyers flasks containing 50 mL of substrate and an inoculum of 5% (m/v). The results indicated that the main groups of microorganisms LAB, AAB and yeasts were able to develop in the fruit juices and coconut water. The highest viable counts were detected in orange juice (7.5 Log CFU/mL of LAB, 6.2 Log CFU/mL of yeast and 7.1 Log CFU/mL of AAB). Total titratable acidity increased for the juice samples and coconut water. There was a decrease of the soluble solids content, reducing sugars and total phenolic compounds for the samples. An increase of the number of VOCs was also observed after fermentation for fruit juices and coconut water. Two esters compounds deserve to be highlighted: octanaic acid ethyl ester and decanoic acid ethyl ester that represented approximately 60% of the total VOCs in the fermented grape juice. Significant differences were observed for the parameters of color L*, a* and b* in fermented orange juice and coconut water, as demonstrated by ΔE (>3). The results demonstrated that fruits juices and coconut water could be alternative substrates for the production of functional beverage, especially for vegans and lactose intolerant consumers.