Coccidia are environmentally resistant parasites with significant implications for global health and economy due to severe tissue infections they can cause in humans and/or animals. Understanding the transmission and host infection by coccidia requires a close examination of the biomechanical responses of their oocyst form to environmental factors. Our study delved into the effects of a chlorinated household disinfectant and thermal treatment on the oocyst wall, with a focus on Eimeria species as a model of coccidia. For this, we employed fluorescence microscopy to quantify the morphological characteristics and autofluorescence of oocysts. To improve automated data processing, an adapted StarDist model intended for oocyst detection was applied. Complementing our microscopy-based investigation, we used microindentation techniques with a flexible micropipette as a spring to evaluate the rupture force of the oocyst wall under various treatment conditions. Our microscopy findings show a significant reduction in autofluorescence and oocyst apparent area for both Eimeria acervulina and E. tenella, with the most dramatic effects found with combined disinfectant and thermal treatments, indicating impaired wall structure. Our innovative micromanipulation system quantified, for the first time to our knowledge, the rupture force of the oocyst wall, which revealed significant variations in E. acervulina in response to the same treatments, while E. tenella displayed less discernible differences. This work sheds light on the varied effects of chemical and physical treatments on coccidian oocyst features, providing important information about potential changes in responses of such parasites to environmental factors.