Gut health is fundamental for human well-being and prevents chronic degenerative diseases and is influenced by the interaction between gut microbiota and food components. In recent years, interest in phenolic compounds has increased due to their health benefits such as antioxidant, antidiabetic, antimicrobial, anti-atherosclerotic, anti-inflammatory, anticarcinogenic, cardio- and neuro-protective properties. Legumes are an essential source of phytochemicals, particularly flavonoids and phenolic acids, distributed mainly in the seed coat, and have been reported to exhibit multiple biological effects. Flavonoids present in legumes have been shown to regulate metabolic stability and membrane transport in the intestine, thus improving bioavailability. Seed processing such as cooking allows the release of phenolic compounds, improving polyphenols digestion and absorption at the intestinal level, maintaining their protective capacity in the oxidative process at the cellular level, and modulating the gut microbiota. All these actions improve gut health, avoiding diseases like irritable bowel syndrome, inflammatory bowel disease, obesity, diabetes, colitis, and colorectal cancer. The effect of the consumption of legumes such as chickpea, pea, and bean, as well as the contribution of phenolic compounds to gut health, will be reviewed in this study.