The impact of milk fortification on the microbiological and physicochemical properties of a set-type skimmed yoghurt using three commercial soluble prebiotics (inulin, iso-malto-oligosaccharides, and xylo-oligosaccharides) at either 3 or 5 g/kg was assessed. The three prebiotics had an insignificant impact on yoghurt fermentation because all yoghurt samples had similar titratable acidity and similar pH values after their lactic acid fermentation. Regarding the control yoghurt samples without prebiotics usage, the prebiotics-fortified yoghurt samples showed no difference in their main chemical compositions, hardness, syneresis extent, and apparent viscosity (p > 0.05), but had a slightly higher lactic acid content and a viable quantity of starter strains. All yoghurt samples had the same acetic acid content, while propionic and butyric acids were not produced. Yoghurt storage at 4 C for 21 d gave these yoghurt samples decreased pH values and a viable quantity of starter strains (especially Lactobacillus delbrueckii subsp. bulgaricus) and unchanged acetic acid; however, it increased lactic acid contents. Overall, prebiotics fortification up to 5 g/kg had a completely insignificant impact on the fermentation and quality attributes of yoghurt samples but could possibly improve the health of consumers due to higher dietary fibers and starter strain populations.