The present study aimed to describe the natural trend of Eimeria spp. oocysts shedding in different breeds of adult goats raised in a sub-Alpine ecosystem by quantitative copromicroscopic analysis. A 1-yr long longitudinal study was planned in a goat herd composed of non-native (Alpine) and autochthonous (Nera di Verzasca) breeds. FLOTAC double technique was implemented to analyze individual fecal samples collected monthly from 2 groups (non-native and native) of 10 goats each. A generalized linear mixed model, in which each goat was included as a random intercept effect, identified 4 predictors of logarithmically transformed oocysts per gram shedding: the number of days from parturition (F = 27.744; P < 0.001), the interaction between the goat breed and the number of days from parturition (F = 8.407; P = 0.004), the interaction between the number of days from parturition and the number of parturitions (F = 6.371; P = 0.012), and the interaction between the monthly rainfalls and temperatures (F = 4.536; P = 0.023). These results indicate that the physiological status (number of days from parturition) of adult goats and its interaction with other individual features (number of parturitions and breed) can affect Eimeria spp. oocysts shedding. Besides, a combination of climatic variables can pose a risk for Eimeria spp. infection in goats reared in the sub-Alpine environment.