The breed of chicken, type of meat portion and cooking had significant effects on the levels of all bioactive compounds analysed in this experiment (p < 0.05). KNCs can be considered a better source of carnosine, anserine, and carnitine compared to CBs. Breast meat showed significantly higher histidyl dipeptide contents, whereas leg meat had higher betaine and carnitine contents (p < 0.05). Cooking of chicken meat caused significant losses in the contents of all endogenous compounds (p < 0.05). The results of this study are very important to breeders, producers, and consumers of poultry because no scientific literature comparing these endogenous bioactive compounds in meat from CBs and indigenous chickens, particularly KNCs, had been published prior to this study.