Our research on the expression and characterization of exosomal miRNAs in buffalo milk, particularly in the context of healthy, sub-clinical mastitis and pasteurized milk, is a novel contribution to the field. We are the first to investigate the expressions of miRNAs and the characterization of exosomes in boiled and pasteurized milk. This study is based on clinical signs and CMT, where twenty buffalo milk samples were divided into normal and sub-clinical mastitis and a third group of ten commercial pasteurized milk. The SCC differed significantly (p < 0.001) in all the groups before boiling. The data analysis demonstrated elevated differential expression of miR-148a and miR-186 in sub-clinical mastitis and pasteurized milk compared to normal milk before and after boiling. The positive correlation between SCC and miR-148a and miR-186 expression indicates their potential as robust biomarkers for sub-clinical mastitis in buffaloes. The miR-148a and miR-186, known to play roles in various diseases like cancer, can withstand commercial pasteurization and boiling, raising the intriguing possibility of transferring through milk exosomes. This finding underscores the need for clean milk production and the importance of understanding the mechanisms of miRNA transfer between species, which is crucial for the future of animal health and milk production.