Lactic acid bacteria (LAB) and propionic acid bacteria (PAB) are known for the production of several important nutraceuticals. We screened 151 LAB and 100 PAB of different origins (fermented foods and feeds) for extracellular folate and intracellular vitamin B12 production in supplemented whey permeate using a standardized microbiological assay (folate) and HPLC (vitamin B12). Five LAB strains belonging to the species Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus brevis and Lactobacillus fermentum exhibited high extracellular folate productions, with a maximum yield of 397 ± 60 ng mL −1 for L. plantarum SM39. The highest vitamin B12 production was measured for Propionibacterium freudenreichii DF15 with 2.5 μg mL −1. Screening a large biodiversity of LAB and PAB led to a representative image of the distribution of folate and vitamin B12 production by these genera and enabled the identification of high natural folate and vitamin B12 producing strains with high potential for applications in fermented foods.