•Short peptides, peptide analogues, and flavonoids were synthesized in the beverage.•Flavonoid glycosides and soyasaponins were degraded in the beverage.•Soy glycerophosphoserines (PS) and glycerophosphoethanolamines (PE) were synthesized.•The beverage showed high ACE inhibitory and DPPH radical scavenging activity.•Lactobacillus, S. cerevisiae, Pichia membranifaciens were among the main microbiome. Integrated metabolomic and metagenomic techniques were used to study the metabolite dynamics and phytochemistry of a soy whey-based beverage bio-transformed by water kefir consortium. The UPLC- MS/MS and HPLC-ESI-MS metabolite quantification and the OPLS-DA result showed that the kefir consortium induced a significant change in the metabolite composition and altered the phytochemistry of the fermented beverage. Bioactive peptide analogues, flavonoids, and glycerophospholipids including N-acetyl-L-phenylalanine, acetyl-DL-leucine; tephcalostan, wogonin, pelargonin, genistein, daidzein, and glycerophosphoserines (PS), glycerophosphoethanolamines (PE) respectively were synthesized while flavonoid glycosides and soyasaponins were degraded in the novel beverage. Furthermore, the beverage showed high ACE inhibitory and DPPH radical scavenging activity of 92.31% and 87.51% respectively. Lactobacillus, Saccharomyces cerevisiae, and Pichia membranifaciens were the predominant microbial groups in the new beverage as revealed by the metagenomic sequence analysis. The study thus provides discrete data evidence that kefir consortium is a viable starter for transforming soy whey into a bioactive beverage.