Microparticulated whey protein (at 0.5 g/100 mL) and two physically modified starches (modified barley and rice; at 0.5, 1.0 g/100 mL) were separately added as clean label ingredients to yogurt to investigate their effects on yogurt properties. The results demonstrated that all five yogurt systems had high water-holding capacity and viscosity, with the one with 1.0 g/100 mL modified barley starch having the highest water-holding capacity (70.20%) and highest viscosity (4 422 mPa·s). In addition, the particle size distribution and rheological analyses consistently showed that modified barley starch had a positive effect on the stability of yogurt. The yogurt with microparticulated whey protein was slightly but not significantly inferior to those with modified starches in all the parameters analyzed.