Pulses are an important source of proteins, but their nutritional quality is limited by anti-nutritional factors and low digestibility of indispensable amino acids. Fermentation offers a strategy to enhance the nutritional value of pulse proteins by decreasing anti-nutritional components and modifying protein structure. This study examined the effects of solid-state fermentation with Bacillus subtilis for 12 and 48 h on protein content, amino acid composition, protein and individual amino acid digestibility, and anti-nutritional components, including phytic acid and total phenolic compounds, in common beans, lentils, and chickpeas. Prolonged fermentation was associated with apparent increases in protein content when expressed on a dry-weight basis, and induced pulse- and time-dependent shifts in amino acid profiles. Fermentation induced a redistribution of indispensable amino acids, with increases in tryptophan, phenylalanine, and cysteine, accompanied by decreases in other amino acids such as leucine and arginine, depending on pulse type and fermentation time. Short-term fermentation (12 h) improved amino acid digestibility and increased the digestible indispensable amino acid scores (DIAAS) in chickpeas across age groups. Digestibility was overall maintained in beans and largely preserved in lentils, except for limited decreases in specific amino acids. In contrast, extended fermentation (48 h) generally reduced amino acid digestibility, most notably in lentils. Reductions in anti-nutritional factors occurred early during fermentation, particularly in lentils and beans, and coincided with maintained or improved digestibility depending on the pulse. Despite these compositional and digestibility changes, the DIAAS of all samples remained below the FAO threshold of 75%, precluding protein quality claims. Overall, these findings highlight the dual role of fermentation as both an enhancer and modulator of protein quality. Optimizing fermentation parameters, particularly duration, may maximize nutritional benefits. When combined with complementary strategies, fermentation holds promise for improving the protein quality of pulses.