This work covers soymilk fermentation by starter and probiotic cultures and explores the influence of cooling protocol on cell viability, organic acid production, sugar consumption, fatty acid profile, and cell survival to in vitro gastrointestinal stress. After fermentation at 37°C by mono-or co-cultures of Streptococcus thermophilus (St), Lactobacillus bulgaricus (Lb), and Lactobacillus paracasei (Lp), fermented soymilk was cooled directly at 4°C for 28 days or cooled in two phases (TPC), i.e., by preceding that step by another at 25°C for 8 h. Soybean milk fermentation by Lb alone lasted longer (15 h) than by StLb or StLbLp (9 h). In ternary culture, TPC increased Lp viability, linoleic, and lactic acid concentrations by 3.8, 22.6, and 96.2%, respectively, whereas the cooling protocol did not influence Lp and St counts after in vitro gastrointestinal stress.