Pulses have desirable nutritional properties and a wide range of applications in the food industry as meat-free, casein-free, gluten-free, and functional food products. Unfortunately, the legume raw material contains some anti-nutrients and allergenic agents; nonetheless, fermentation processes may reduce some of these undesirable compounds. Therefore, the objective of the preliminary investigation was to determine the profile of bacteria occurring after spontaneous fermentation of Lens culinaris Medik. and detect changes in the protein–peptide pattern, including potential modifications of Len c3, i.e., a non-specific lipid-transfer protein (nsLTP) recognized as an important allergen. This study involved MALDI TOF/TOF, Illumina next-generation sequencing, and FT-IR spectroscopy analyses. Sixteen different species were identified in the plant-based material after 48-h spontaneous fermentation. The most abundant species were Lactococcus taiwanensis and Pediococcus pentosaceus (54.95% and 25.34%, respectively). The performed initial analysis revealed that after spontaneous fermentation had occurred the degradation of proteins (~10 kDa) and peptides (6–8 kDa), as well as the decomposition of proteins in the mass range that might be attributed to allergenic nsLTP. The preliminary findings encourage further research into the functional and technological properties of the isolated bacteria and in-depth analyses of the possibility of the removal of allergenic compounds from red lentils through fermentation carried out by the isolates.