Soy‐based fermented beverages prepared with potential Lactobacilli provide nutrition with various health beneficial attributes like ACE inhibitory, antioxidative, anti‐microbial activities to the human host. Further, the biotransformation of isoflavones through soy lacto‐fermentation also produces extra benefits to the hosts by preventing hormonal disorders in the post‐menopausal women. In the present study, storage stability and biofunctional properties of the fermented soy‐based beverages (A1 prepared with L. fermentum (M2), A2 prepared with L. casei (NK9), A3 prepared with (M2 + NK9)) were evaluated during the storage upto 15 days at refrigerated temperature (5 ± 2°C). ACE inhibitory (A1: 71.11, A2: 60.33, A3: 75.53%), antioxidative activity (A1: 36.67, A2: 43.84, A3: 53.62%), and antimicrobial activity were significantly (p < .05) highest for all the fermented soy‐based beverages (A1, A2, A3) than control (A0: ACE inhibitory activity: 20.51% and antioxidative activity: 21.37%), respectively. Biotransformation of isoflavones was also evaluated during storage. A3 showed the highest biotransformation of soy aglycones (Daidzein: 1.25 mg/100 ml and Genistein: 2.65 mg/100 ml) in the fresh soy‐based fermented beverage. During the storage study (upto 15 days), biofunctional properties decreased slightly upto 5th day. However, functional fermented soy‐based beverages were developed with various health‐promoting attributes through in vitro study using potent Lactobacillus cultures. Practical applications Fermented soy‐based beverages were prepared using SMP (Skim Milk Powder) and WPC‐70 (Whey Protein Concentrate‐70) as milk ingredients to provide extra nutrition to the lactic acid bacteria during fermentation and also to improve the concentration and value addition to the beverages. A3 beverage (supplemented with 2.0% SMP and 1.5% WPC‐70) fermented with L. fermentum and L. casei exhibited highest biofunctional properties due to maximum symbiosis association of both the cultures than control during the storage at refrigerated temperature (5 ± 2°C) with better storage stability. Hence, functional fermented soy‐based beverage supplemented with milk‐based ingredients could be a nutritive health drink for people of all age groups.