The impact of calcium fortification, delivered using different proportions of soluble (calcium chloride; CaCl₂) and insoluble (micronised calcium citrate; CaCit) calcium salts, on physicochemical and thermal stability properties of a model infant milk formula (IMF) was determined. The IMF was formulated with a whey protein fraction dominant in α-lactalbumin and fortified with calcium (1500 mg L⁻¹) using 70:30, 60:40, 50:50, 40:60 and 30:70 ratios of CaCit:CaCl₂. Increasing CaCl₂ levels decreased the net zeta-potential of IMFs from −41.0 to −22.1 mV and increased ionic calcium levels (1.44–6.99 mM). The apparent viscosity, especially at acidic pH (6.40), increased compared to the control with values ranging from 22.3 to 50.2 mPa s for ratios 70:30 and 30:70, respectively. In addition, mean particle size of the IMF increased, with values ranging from 2.19 to 43.4 μm. This study provides useful information in supporting next-generation fortification strategies of nutritional dairy-based products with calcium.