Water kefir microbiota was used to develop novel soy whey‐based beverages that have antioxidant activity. In the present study, comparative phenolics, antioxidant and metagenomic composition of the soy whey beverages fermented using three different water kefir microbiota, named WKFS‐A, WKFS‐B and WKFS‐C were investigated. WKFS‐B beverage had the highest concentrations of isoflavone aglycones (208.73 ± 2.78 mg L⁻¹) and phenolic acids (132.33 ± 3.41 mg L⁻¹) compared with WKFS‐A (193.88 ± 1.15 mg L⁻¹) and (91.73 ± 2.34 mg L⁻¹) and WKFS‐C (160.63 ± 1.76 mg L⁻¹) and (97.13 ± 2.63 mg L⁻¹), respectively. The WKFS‐B also showed higher DPPH and ABTS radical scavenging activity and ferric reducing antioxidant power compared with WKFS‐A and WKFS‐C beverages. Microbial species diversity index analysis showed that a higher concentration of isoflavone aglycones, phenolic acids and increased antioxidant activity in the WKFS‐B beverage correlates with the higher relative abundance of Lactobacillus genus. This study thus revealed that Lactobacillus dominated water kefir microbiota produces soy whey beverages with high phenolic acids, isoflavone aglycones and antioxidant activity.