The subcritical water extraction (SWE) method, as a proper alternative to conventional methods due to low cost, short processing time, environmental sustainability, and mild operating conditions, has been applied to produce valuable materials from different biomass. Rice milling byproduct (RMB) as abundant and locally available agricultural wastes is normally used for extracting oil and as animal feed. In this study, the quality and quantity of valuable compounds extracted by the SWE were investigated to select the optimum SWE conditions and the best extract to produce healthy cereal-based milk analogs. The most appropriate SWE parameters were investigated by the combined design method were 130°C and 45 min, rice bran: broken rice ratio of 10:90, the solid-water ratio of 0.12, and a particle size of <710 μm, respectively. SWE positively affected the release and production of some bioactive compounds such as total phenolic, flavonoids, organic acids. The milk analogs consisted of the optimum RMB extract, inulin, and Persian grape molasses (as a sucrose alternative) were then fermented by either Lactobacillus casei or Lactobacillus plantarum (0.5 McFarland). The fermentation process also rose the values of some nutrients, including vitamin B (B3, B6, and B9), organic acids, total phenolic compounds, and flavonoids. it decreased the contents of monosaccharides (p < .5), while the increased content of alcohol was negligible (<0.3%). Compared with L. plantarum, L. casei had a higher impact on the production of these bioactive compounds and more considerably increased antioxidant activity of the related beverages; nevertheless, beverages containing L. plantarum had the greatest over-acceptability. Moreover, the survival of L. casei and L. plantarum in beverages was in the standard range (106–108 CFU/ml) during storage, demonstrating that RMB ingredients along with inulin can positively affect LAB survival. Novelty impact statement The innovative aspect of this work is related to the use of Iranian agricultural byproduct such as BRM and Persian Grape Molasses in production of milk analogs containing Persian type culture collection and the use of subcritical water extraction as an environmentally friendly method for the production of functional beverages.