Germination is a bioprocessing technique used by the food industry to improve the nutrient content of seeds. Imbibition is considered a crucial stage for optimal plant development. In this research, four different groups of seeds were studied to evaluate the effect of using probiotics during the imbibition phase on the germination process, as well as on the microbiological quality, as specified by Mexican regulations. The efficiency of probiotic production was also determined. Regarding the results, most seeds achieved a germination rate between 90–100%, with seeds inoculated with probiotics reaching a higher rate. This increase was related to the concentration of auxins. Importantly, the lowest levels of CFU/g counts for coliforms and fungi were found in the treated sprouts. Additionally, the sprouts exhibited values greater than 1 × 10⁶ CFU/g of probiotics. The imbibition of certain types of seeds with probiotics with Lactiplantibacillus plantarum and Saccharomyces boulardii increases the germination speed, as well as the biomass obtained, which suggests that it may be an alternative to treatments in the agricultural industry for greater production.