The effect of enzymatic deamidation on the textural and microstructural properties of set yoghurts with different fat contents was investigated. Low-fat yoghurts were prepared with various protein-glutaminase (PG) concentrations. Textural analysis results showed that PG treatment decreased the firmness of non-fat and low-fat yoghurts and that adhesiveness increased due to PG treatment, regardless of fat content. With the increase in the degree of deamidation, syneresis on the surface of the non-fat and low-fat yoghurt decreased, and the surface appeared to be smooth and glossy. The microstructure of set yoghurt gels was observed using confocal laser scanning microscopy. PG-induced deamidation resulted in the yoghurt gel being more coherent and thicker, regardless of fat content. These observations can be attributed to the increase in carboxyl groups on caseins. More hydrophilic caseins resulted in a decrease in the ability to self-associate, thereby decreasing the cohesive forces between casein micelles.