Milk yield and its composition show individual variation due to the effects of the environment. Previous studies suggest that meteorological variables exert negative effects on milk yield and composition, especially during summer. This study aimed to examine the effects of meteorological variables on bulk milk composition in the Sardinian sheep production system. In this work, a total of 218,170 records belonging to 4562 dairy sheep farms were merged with the meteorological data provided by 60 meteorological stations located on Sardinia Island (Italy). Milk composition in the late spring and summer recorded during a 5-year period was used to evaluate the impact of climate exposure on bulk milk traits. The milk quality was analyzed using a linear mixed model that included the fixed effects of the year of sampling, the flock size, the temperature humidity index (THI) and the random effect of the flock. The variability of milk composition explained by flock and management ranged from 30 to 64%. The flock size exerted a significant effect on milk composition: large flocks characterized by advanced management and feeding techniques resulted in higher milk quality (e.g., higher protein and fat, lower lactose) compared to traditionally managed small flocks. The impact of THI on milk composition was statistically significant across different milk quality traits (p < 0.001); the effect of thermal stress varied according to the month of lactation. For instance, milk fat content in May increased by +0.4% for THI > 76. In June, no relevant differences were observed, whereas a decrease in fat percentage was observed in July as THI values increased (up to −0.5% for THI > 76). While somatic cell counts remained relatively stable across different conditions, total bacterial count showed greater seasonal variability, peaking during warmer periods. In addition, using factor analysis, we developed a multivariate meteorological index (MMI), which explained 51% of the variance of the original meteorological data. MMI was highly correlated with THI (r = 0.75). The same linear mixed model applied for modeling THI was used to assess the effect of MMI on milk traits. Fat, protein fractions and lactose showed significant variation across MMI classes (p-value < 0.001) in the same direction as those based on THI. Overall, our findings underscore the impact of both flock size and environmental conditions on milk quality, with heat stress and traditional versus modern management practices leading to measurable differences in milk traits.