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 degrees 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 degrees 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.