Given that mung beans constitute a significant nutrient source in many cultures, it is worthwhile to investigate ways to improve their nutritional and functional properties. The effect of fermentation of mung beans by Bacillus subtilis subsp. natto was investigated in various reactor designs, including static, shaking flasks, and soft elastic tubular reactors (SETR). The results showed that all three processes might affect the substrate, resulting in changes in the protein and carbohydrate fractions. We noticed an increase in soluble protein and serine levels, which we attribute to the proteases produced during fermentation. Through XRD, FTIR, and DSC analyses, it was also discovered that whereas static and shaking flask fermentation might raise relative crystallinity and peak temperature, fermentation performed on the SETR decreased these values. It was also possible to notice that SETR might induce a change in the particle size distribution of the substrate through a complex impact of mechanical forces, mixing, and microbial activity, which could be helpful to some aspects of the process. To summarize, fermentation of mung beans by Bacillus. subtilis subsp. natto could be an attractive approach for producing a food ingredient with various functional and nutritional properties. Furthermore, the SETR has been shown to be a viable technique for dealing with high solid load substrates, whether as the reactor for the entire process or as a first stage/pre-treatment step, and its applicability in bioprocesses should be explored further.