Comfort-type infant formula (IF) emulsions are frequently manufactured using whey protein hydrolysate (WPH) ingredients; however, stability of these emulsions to heating is often poor. The objective of this study was to improve heat stability of such emulsions by conjugation of WPH with maltodextrin (MD) through wet heating. Model IF emulsions (1.55% protein, 3.50% oil, 7.00% carbohydrate) were prepared using whey protein isolate (WPI), WPH, heated WPH or WPH-MD conjugate. The conjugate was prepared by heating a WPH/MD solution (5.00% protein and 5.00% maltodextrin, pH 8.2) at 90°C for 8 h; heated WPH was prepared in a similar manner but in the absence of MD. Emulsions were heated at 75°C or 95°C for 15 min using a rheometer, with viscosity data recorded throughout the heat treatments, or at 100°C for 15 min using an oil bath. Emulsions were recovered after all heat treatments and changes in viscosity, fat globule size distribution (FGSD) and microstructure, determined using confocal laser scanning microscopy (CLSM), were used to monitor the effects of heating on the structure/stability of the emulsions. Emulsions with similar, monomodal size distributions (mean oil droplet diameter ≤ 1.0 µm) were formed with all protein ingredients (no significant differences, P < 0.05). Heat stability of emulsions increased in the order WPH < WPI ≪ heated WPH ⋘ WPH-MD conjugate. A sharp increase in viscosity during heating at 75°C (WPH) or 95°C (WPI) and significantly higher viscosity (P < 0.05) post-heat treatment (as compared with initial viscosity) indicated structural rearrangement/coagulation in the WPH and WPI stabilized emulsions; no changes in viscosity on heating were observed for emulsions stabilized with heated WPH or WPH-MD conjugate. After heat treatment at 100°C, flocculation and coalescence of oil droplets in emulsions stabilized by heated WPH were mediated by protein aggregation (as evidenced by CLSM analysis) while no changes in FGSD or microstructure were observed in emulsions stabilized by WPH-MD conjugate. Modification of WPH through conjugation with MD yielded a protein ingredient with superior thermal stability in oil-in-water IF emulsions.