Eimeria species, the causative agents of avian coccidiosis, are major pathogens in poultry, resulting in substantial economic losses and welfare concerns worldwide. Understanding their complex life cycle, including different developmental stages and host interactions, is essential for advancing control strategies. Traditional cultivation systems, such as primary cell cultures and immortalised cell lines, have provided valuable insights, but they present limitations in supporting complete parasite development, host–pathogen interactions and immune response evaluation. Recent advances in intestinal organoids offer a promising alternative for Eimeria research. Initially developed in human models, intestinal organoids have been successfully adapted to avian systems, replicating the architecture, cellular diversity and physiological functions of the chicken gut epithelium. These 3D models provide now a physiologically relevant platform for studying parasite development, host–pathogen interactions, immune responses and drug screening in vitro. Complementary tools, such as intestinal explants, could further enhance the experimental repertory available for investigating Eimeria species. Additionally, insights from studies on related apicomplexan parasites support the translational value of these systems. These innovative systems could support significant advances in Eimeria cultivation, enabling more robust and ethical research while reducing the use of experimental animals.