Calcium binding to peptides formed by hydrolysis of whey proteins during digestion is important for calcium uptake in the intestines and affects the antioxidant function of the peptides. For the two dipeptides, Gly-Tyr and Tyr-Gly, potential hydrolysis products of α-lactalbumin, calcium binding to the three forms of each dipeptide in acid-base equilibrium at intestinal pH was determined electrochemically and compared to binding to tyrosine for aqueous 0.16 M NaCl for 5 < pH < 9 at 15 °C, 25 °C, and 37 °C. At milk pH at 25 °C, binding of calcium to the zwitterion of GlyTyr dominates, with an association constant K_ass2 = 22 M⁻¹ with ΔH⁰ = −46 kJ·mol⁻¹, while binding to the mononegative TyrGly dominates for TyrGly with K_ass3 = 32 M⁻¹ and ΔH⁰ = −38 kJ·mol⁻¹. At intestinal conditions, pH = 7 and 37 °C, binding of calcium has similar affinity for GlyTyr and TyrGly, while at higher pH and lower temperature, GlyTyr binds stronger. Density Functional Theory calculations confirmed a stronger binding to the zwitterion of GlyTyr than of TyrGly and an increasing affinity with increasing pH for both. Calcium binding to the acid/base forms of the dipeptides is at neutral pH strongly exothermic with ΔH⁰ becoming less negative at higher pH, and a linear enthalpy–entropy compensation (r² = 0.99) results in comparable binding important for calcium bioavailability along the changing distribution among acid-base forms. Calcium binding decreases radical scavenging rate and antioxidative activity of both dipeptides.