Various species of Eimeria infect the intestinal tract of poultry, with Eimeria maxima commonly associated with the development of necrotic enteritis (NE). Restrictions to prophylactic use of Category 2 antibiotics in Canadian poultry make outbreaks of NE caused by Clostridium perfringens more likely. Infections with Eimeria species, combined with poor diet and sanitation, are key drivers of C. perfringens infection and NE. This study quantified C. perfringens and E. maxima DNA from within the intestinal tract of experimentally infected broilers using a newly developed, duplexed, probe-based qPCR assay. C. perfringens showed little change in quantification but expressed lesion development in birds infected with E. maxima, particularly from 5 days-post-infection. Inoculation of day-of-age chicks with C. perfringens permitted colonization and persistence throughout the intestinal tract for several weeks. Birds inoculated with C. perfringens prior to E. maxima, and vice versa, were more likely to exhibit lesions consistent with NE.