The effects of cooking treatments (boiling, autoclaving and microwave cooking) and germination on the nutritional composition and antinutritional factors of chickpeas were studied. Cooking treatments and/or germination caused significant (p < 0.05) decreases in fat, total ash, carbohydrate fractions, antinutritional factors, minerals and B-vitamins. Germination was less effective than cooking treatments in reducing trypsin inhibitor, hemagglutinin activity, tannins and saponins; it was more effective in reducing phytic acid, stachyose and raffinose. Cooking treatments and germination decreased the concentrations of lysine, tryptophan, total aromatic and sulfur-containing amino acids. However, cooked and germinated chickpeas were still higher in lysine, isoleucine and total aromatic amino acid contents than the FAO/WHO reference. The losses in B-vitamins and minerals in chickpeas cooked by microwaving were smaller than in those cooked by boiling and autoclaving. Germination resulted in greater retention of all minerals and B-vitamins compared to cooking treatments. In vitro protein digestibility, protein efficiency ratio and essential amino acid index were improved by all treatments. The chemical score and limiting amino acid of chickpeas subjected to the various treatments varied considerably, depending on the type of treatment. Based on these results, microwave cooking appears to be the best alternative for legume preparation in households and restaurants.