Mastitis significantly impacts dairy goat herds, causing substantial economic losses. The escalating challenge of multidrug-resistant bacteria has prompted research into alternative therapeutic strategies, including milk microbiota transfer and phytochemical treatments. This study evaluates milk chemical elements as potential biomarkers during alternative treatments for Staphylococcus warneri-induced goat mastitis. Seven female Parda Alpina goats were studied, with six receiving sequential treatments: milk microbiota transplantation (MMT) from the seventh goat (donor), two days later, intra-mammary 7-epiclusianone administration followed. The right udder of the six goats received the treatments and different time points while the left udder served as the control. Milk samples (n = 120) were analyzed using X-ray Energy Dispersive Spectroscopy (XEDS) to monitor trace and macro elements. Milk elemental level variations were observed across both treatments. Notable changes included increased iron levels from MMT initiation, reduced copper and zinc levels during MMT, and decreased sodium levels following 7-epiclusianone treatment. These results suggest zinc, copper, iron, and sodium could serve as potential biomarkers for monitoring mastitis treatment effectiveness. Additional research with broader and more diverse sample populations would help validate these findings and explore the method's broader applicability.