Foodborne diseases are a global public health concern. Toxoplasma gondii is considered as one of the most of concern parasites in the world due to its multiple routes of transmission, high prevalence, and global distribution. The T. gondii oocyst the environmental form of the parasite, is known to remain infective for very long periods in soils and waters. These reservoirs can be sources of contamination during the primary production of vegetables, fruits, and seafood. In order to reduce human exposure, food industries implement control measures whose efficiency to inactivate the pathogens in the food matrix requires evaluation. However, for T. gondii, such studies face methodological and financial constraints. Indeed, sourcing infective oocysts in large quantities and measuring their infectivity are costly, require specific expertise and authorizations, and raise ethical and biohazard issues. Therefore, identifying and characterizing organisms that could be used as surrogates for T. gondii oocysts is a critical issue for the agri-food industry. The ideal surrogate should be non-pathogenic, easy to produce in large quantities and its viability/infectivity easily measured in the laboratory to assess control measures inactivation efficiency. The surrogate should display comparable or less inactivation to T. gondii oocysts, as well as similar inactivation kinetics. Whenever possible, the model should be equivalent in structure and size to the target pathogen and have a similar mode of transmission in the matrices to be studied. In this study, oocysts of the genus Eimeria were evaluated as surrogates of T. gondii. Physical and chemical treatments were applied to Eimeria acervulina and Toxoplasma oocysts and their impact on their structure was evaluated by flow cytometry and microscopy. The following parameters were studied: integrity (size/granulometry) and permeability, measured by the incorporation of different markers such as lectins. The first data obtained suggest that Eimeria acervulina would be a good model to study T. gondii for certain treatments.