The salt fractions of milk consist of cations (e.g., Ca, Mg, and Na) and anions (e.g., phosphate, citrate, and chloride). These salts are present as free ions or in complexes with other ions or proteins, primarily the caseins. Furthermore, significant levels of Ca and phosphate are also found in insoluble form, inside the casein micelles. The distribution of salts between this micellar phase and the soluble phase is important for the stability and properties of milk and dairy products. Various processes, such as (ultra-)centrifugation, (ultra-)filtration, dialysis, and selective precipitation have been used to separate the micellar and soluble phases in milk and dairy products to allow for studying the salts’ distribution between these phases. These different methods can lead to different levels of soluble salts because the salts in the supernatant from centrifugation, the permeate from ultrafiltration, and the diffusate from dialysis can differ notably. Hence, understanding which components are fractionated with these techniques and how this affects the levels of the soluble salts determined is critical for milk and dairy products. Applying the aforementioned methods to cheese products is further challenging because these methods are primarily developed for fractionating the soluble and micellar phases of milk. Instead, methods that analyze salts in water-soluble extracts, or soluble phases expressed from cheese by pressing or centrifugation are typically used. This review focuses on the significance of salt distribution and variations in salt fractions obtained using different methodologies for both milk and cheese.