Major histocompatibility complex (MHC) congenic chicken lines have been used as a model to study infectious bronchitis virus (IBV) immune responses in chickens. Zinc (Zn) and manganese (Mn) are trace minerals that act as enzyme cofactors in cellular reactions. In addition, Zn is an important modulator of immune responses, especially in the respiratory tract. Zinc and Zn + Mn amino acid complex supplements were tested to alleviate the effects of an IBV challenge using relatively resistant and susceptible MHC congenic chicken lines. Prior to the challenge with IBV, the amino acid–bound supplements induced better weight gain in the IBV-resistant chicken line (331/B2) compared to the birds fed with the sulfate-delivered supplements. No body weight differences were detected between IBV-challenged and unchallenged 331/B2 birds supplemented with Zn in amino acid complex. A reduction of respiratory signs was observed in 335/B19 birds fed with the diet supplemented with Zn in amino acid complexes at 4 dpi. Compared to the sulfate-bound trace minerals, 331/B2 chickens fed with the amino acid–bound supplements presented milder clinical sign trends at 6 dpi and less severe airsacculitis at 14 dpi. The total antibody response in serum in 331/B2 birds fed with the amino acid–bound Zn ration was the highest among all groups tested. Both amino acid–delivered trace mineral supplements induced a slightly higher antibody response than the sulfate-bound ration in both chicken lines. This experiment provides insights into the effect of Zn and Mn on the immunity of chickens with known different susceptibilities to IBV.