Free fluoride ions are effective in combating caries in children, and their supplementation in milk has been widely used worldwide for this purpose. Furthermore, it is known that ionic fluoride added to milk is distributed among its components, but little is known about their quantitative relationships. This is likely due to the absence of an analytical protocol aimed at differentiating and quantifying the most important forms of fluorine present in milk. For the first time, a comprehensive protocol made up of six potentiometric methods devoted to quantifying the most important fractions of fluorine in milk (i.e., the free inorganic fluoride, the inorganic bonded fluorine, the caseins-bonded fluorine, the whey-bonded fluorine, the lipid-bonded fluorine, and the total fluorine) has been developed and tested on real samples. Four of the six methods of the procedure are original, and all have been validated in terms of limit of detection and quantification, precision, and trueness. The data obtained show that 9% of all fluorine was in ionic form, while 66.3% of total fluorine was bound to proteins and lipids, therefore unavailable for human absorption. Beyond applications in dental research, this protocol could be extended also to other foods, or used in environmental monitoring.