It is largely unknown how processing affects bioactive potential of chickpea proteins to prevent bowel inflammatory diseases. The aim was to investigate the anti-inflammatory activity of protein concentrates from germinated and cooked chickpeas (GC and CC, respectively) and its relationship with protein and isoflavone composition before and after in vitro gastrointestinal digestion and absorption. Anti-inflammatory activity of GC digests was almost 2-fold higher than CC digests (p < 0.05), which was associated to greater content of peptides, formononetin and biochanin A (p < 0.05). Anti-inflammatory activity of phenolic fraction in digests was 7-fold higher than the protein fraction (p < 0.05). The most active peptide fraction from GC digest (IC50 = 93 µg/mL) contained a total of 24 peptides derived from legumin and vicilin. In conclusion, this study stands out the potential of germinated chickpea proteins concentrates to exert anti-inflammatory effects in the lower gut which may contribute to the prevention of bowel inflammatory diseases.