The growing demand for fermented plant-based foods has intensified interest in exploring native lactic acid bacteria (LAB) with enhanced technological and bioactive properties. This study investigate the spontaneous fermentation of red lentils, focusing on microbial succession, biochemical shifts, and riboflavin-producing strains. Over 48 h, fat content declined from 0.175 ± 0.18 % to 0.107 ± 0.14 %, and protein content from 3.61 ± 0.01 % to 2.61 ± 0.01 %. At the same time, bioactive peptide formation increased markedly, while bitter-tasting amino acids—tyrosine (to 0.68 ± 0.01 mg/g), histidine (0.62 ± 0.02 mg/g), and isoleucine (0.88 ± 0.04 mg/g)—decreased. Molecular analysis via PCR-DGGE revealed a shift from Leuconostoc lactis dominance at 24 h to Weissella confusa/cibaria and Pediococcus pentosaceus at 48 h. Correspondingly, riboflavin levels rose from 6.33 ± 0.50 to 9.88 ± 0.15 μg/100 g. MALDI-TOF MS results revealed that all riboflavin-producing isolates from the 48-h fermentation were identified as Weissella cibaria. These data demonstrate that spontaneous red lentil fermentation not only enhances the nutritional profile through peptide enrichment but also serves as a natural, cost-effective strategy for in situ vitamin B2 fortification. This approach represents a promising strategy for the development of next-generation functional plant-based foods, enriched with bioactive compounds and health-promoting potential.