Plant-based milk alternatives are often nutritionally unbalanced, and their flavor profiles limit their acceptance. In this work, mono- and co-culture fermentation processes were developed to upgrade plant milks into more healthy and tasty products. First, two food-grade strains were selected from more than 2,500 candidates by a genome-based approach, which accumulated high levels of L-lysine and, therefore, enhanced the protein quality of plant milk. Subsequently, a novel co-culture process was established to increase the vitamin B₁₂ level to 17 μg (100 g)⁻¹, 7-fold higher than the recommended daily uptake. Finally, the flavor metabolism of lactic acid bacteria during plant milk fermentation was studied. Notably, several food-grade approved strains delivered beneficial changes opening up the possibility of creating new flavors and diversifying plant milk products