Chemical composition and protein quality of raw and heat-processed (boiled and autoclaved) samples of selected advanced breeding lines of lima beans (Tpl 1B, Tpl 7A and Tpl 175A), part of a larger collection developed by the International Institute for Tropical Agriculture (IITA), and evaluated in agronomic field trials in Nigeria, were studied. Protein quality was evaluated using weanling albino rats fed diets which we formulated to supply 10% protein using lima bean samples with casein as a control. Raw seeds contained 24.0–27.8% crude protein, 6.8–7.7 mg iron per 100g, 55.7–79.0 mg polyphenol per 100g and 118.8–225.9 mg phytic acid per 100g seed flour. Tpl 1B had higher crude protein and mineral (calcium, iron and sodium) contents, and lower amounts of polyphenol and phytic acid compared with Tpl 7A and Tpl 175A. Boiling (moist heat) was more effective than autoclaving (dry heat) for reducing the levels of antinutrients and improving the protein quality of the beans, as shown by the higher values for weight gain, protein efficiency ratio (PER), net protein ratio (NPR) and true digestibility (TD) of boiled samples. There were no significant (p > 0.05) differences between the values obtained for PER, NPR, and TD of diets formulated with boiled samples of Tpl 1B and casein, indicating the superiority of the protein quality of this lima bean line compared with Tpl 7A and Tpl 175A.