Seven different types of starch based fat substitutes were used for the production of set‐style yogurt from reconstituted skimmed milk powder. The yogurt milks contained 14.0–15.8% total solids, 7.3–9.1% carbohydrates, 5.3–5.6% protein and 1.0–1.2% ash. The fat content of all the batches was 0.1% except the control (1.5%), which was made with anhydrous milk fat. Yogurts made with P‐Fibre 150 C and 285 F contained 0.5 and 1.1% fibre respectively. Decrease in whey syneresis and increase in firmness in all the yogurts were observed during 20 days' storage at 5°C. Yogurt made with P‐Fibre 150 C had the least amount of whey syneresis. Scanning electron microscopy and transmission electron microscopy revealed subtle differences in the microstructure of set‐style yogurts due to the different starch based fat substitute used. ‘Spikes’ and ‘hair’ like structures were evident around the casein micelles in the milk base. They were lightly stained when compared with the caseins. Their detection in the yogurt was very difficult and only P‐150 C and P‐285 F substitutes were visualized whereas the others could not be detected even when their concentration was increased to 5%. Yogurt made with Lycadex® 100 was more porous and had slightly larger void spaces filled with milk serum. The use of a higher concentration (5%) of fat substitutes increased the firmness, but impaired the flavour