Previous studies have reported on the phytotherapeutic potential of propolis from southern Brazil (Urupema, Santa Catarina State), in particular, its efficacy in the treatment of bovine mastitis. The present study evaluates the effect of seasonal variation on the chemical composition of propolis from southern Brazil and its resultant antimicrobial and cytotoxic activities in the context of treating bovine mastitis. Antimicrobial activity against Staphylococcus aureus was assessed, along with the cytotoxicity and induction of apoptosis in MAC-T bovine mammary epithelial cells. With the exception of spring propolis, the flavonoid quercetin was the main compound present in all samples. The minimum inhibitory concentration (MIC) of propolis against S. aureus from mastitic milk was 140 μg/mL for samples collected during the spring, autumn, and winter seasons, but 280 μg/mL for samples collected in summer. For MAC-T cells, the spring propolis extract was more toxic with an IC50 of 120 μg/mL. However, for 120 μg/mL of spring propolis extract, only 0.77% of necrotic and 37% of apoptotic MAC-T cells were found, respectively. Nonetheless, the induction of cell deaththrough apoptosis by propolis extract suggests less severe damage to bovine mammary glands. Moreover, only negligible seasonal variation was found in the chemical composition of propolis from southern Brazil, and no biological activities were determined to be harmful. Therefore, this propolis shows promise as an alternative to commercial antimicrobials in the control of bovine mastitis, offering support for organic milk production.