Biological processes of legumes may change their nutritional value of lipids, but there is no research on the fatty acid profile and their position distribution in fermented beverages obtained from germinated bean seeds. The present study aimed to determine the effect of fermentation by Lactobacillus strains on the fatty acid profile and their positional distribution in triacylglycerols of beverage obtained from germinated bean “Piękny Jaś Karłowy” (Phaseolus vulgaris) fermented by Lactobacillus strains. The population of lactobacilli (the pour plate method), pH, the fatty acid profile (gas chromatograph with a flame ionization detector), and the positional distribution of fatty acids in triacylglycerols (GC-FID) were determined before and after the fermentation of received beverages. The fermentation of beverages did not change the lactobacilli population (over 7 log10 CFU/g), but changed pH (to 4.7–3.7 or 5.8–5.6), fatty acid profile, and the positional distribution of fatty acids were observed. The fermentation process contributed to an increase in the share of palmitic, stearic, and oleic acids in the fatty acid profile compared to that in raw bean seeds. The fermentation processes changed the share of individual acids in positions sn–1 and sn–3 depending on Lactobacillus strain used. Compared to non-fermented beverages, in most fermented beverages, a lower share of palmitic and stearic acids, as well as a higher share of oleic acid in the sn–2 were observed.