Coccidiosis and necrotic enteritis are among the most common diseases affecting poultry, with economic impact due to reduced production and the costs of treatment and prevention. Eimeria invasion contributes to gut damage that promotes the growth of other harmful pathogens, such as Clostridium perfringens. Coccidiostats, with toltrazuril as an example, are widely used to control these infections. In this study, we assessed the effects of Eimeria spp. infection and coinfection with Eimeria spp. and Clostridium perfringens on chicken weight and toltrazuril concentrations, along with two metabolites—toltrazuril sulfoxide and toltrazuril sulfone—using liquid chromatography coupled with mass spectrometry. The analysis of liver and muscle samples showed lower levels of residues in groups challenged with Eimeria spp. In the case of combined Eimeria and C. perfringens infection, no significant differences were observed. These findings suggest that the combination of Eimeria and C. perfringens does not significantly alter the residue levels of toltrazuril and its metabolites, providing valuable insight into the pharmacokinetics of toltrazuril in poultry under infection conditions. This research contributes to optimizing drug use and residue management in poultry production.