The current research work was carried out to characterize the local (Faisal, NARC-II, Willium-82, Ajmeri and Rawal-I) promising soybean varieties. The physicochemical analysis like protein, fat, ash, minerals and fatty acids profile showed the significant variation. Phytochemical test like TPC, TFC, antioxidant activity (DPPH, ABTS and FRAP) showed substantial variation among them. Lipoxygenase (LOX-1, LOX-2 and LOX-3 that cause oxidation and off- flavor were lower in Ajmeri. The initially three secreened varieties (Ajmeri, Willium-82 and NARC-II) were used to prepare fermented soy milk fermented with Lactobacillus acidophilus and Lactobacillus casei to evaluate their single and coculture effect. The periodically physicochemical, functional, microbial, antioxidant potential and organoleptic evaluation of soy milk showed significant differences among three varieties and treatments of soy milk. The viscosity versus shear rate displayed higher viscosity in coculture fermented soy milk especially in Ajmeri. Scanning Electron microscopy depicted that Ajmeri soy milk fermented with L. caseishowed relatively more uniform texture and smaller pore size in comparison to L. acidophilus however,it was elucidated that combination of cultures depicting constant and precise pore formation with stronger cross linking of soybean protein that had modified structure stability. Isoflavones quantified through HPLC displayed were higher in comparison to genistein in Ajmeri soy milk fermented with co-culture. Afterwards Ajmeri soy milk fermented by coculture and non-fermented was used to conduct bio-efficacy trial on Sprague dawley rats for Hyperglycemia and Hypercholesterolemia. The studies were intended as study I (Normal rats) study II (Hyperglycemic rats and study III (Hypercholestrolemic rats). The results showed percent decrease in glucose level from 3.61 to 17.11% and inclining insulin level from 1.8 to 8.3%. The value added drink was most effective in lowering cholesterol level from 2.62 to 13.51% likewise the LDL reduction and elevation of HDL was increased. The safety test on liver, kidney and blood biochemistry suggested it as a safe and non-toxic product. The research explored that soybeans are a good source of nutritional food and Ajmeri, Willium-82 and NARC- II have food grade value than other varieties. Furthermore, combination of L. acidophilus and L. casei in the fermentation of Ajmeri soy milk has a valuable effect against hyperglycemia and hypercholesterolemia is effective in comparison to non- fermented soy milk. Present study colclueded that soy based functional foods should be encouraged in diet to curb from various health remadies and protein requirement can be fulfilled in an inexpensive way by administrating fermented soy milk.