This research paper assessed textural, microstructural, sensory and colour properties of set-yoghurts produced using milk from two indigenous cattle types, Thamankaduwa White (TW) and Lankan cattle (LC) compared to two generic cattle breeds, Friesian and Jersey. Instrumental texture profile (firmness, adhesiveness, cohesiveness and springiness), colour space (L* a* b*) and scanning electron micrographs of set-yoghurts during 21 d of storage (4 ± 1°C) were evaluated. Sensory quality attributes were evaluated with 40 untrained panellists using a five-point hedonic scale. Set-yoghurts prepared using indigenous cow milk showed higher (P < 0.05) firmness, cohesiveness and apparent viscosity values compared to those prepared using generic cow milk. As revealed by micrographs, set-yoghurts made from TW milk had lesser and smaller void spaces and a dense protein gel network than gels made from LC and the two generic breeds. The gel network made from Friesian milk showed a comparatively larger porous gel structure and thinner protein strands resulting in a weaker gel than other milk gels. The highest lightness (L*) and yellowness (b*) were observed from set-yoghurt produced from Friesian and LC milk, respectively. Set-yoghurts from TW milk had the highest (P < 0.05) sensory scores for all sensory attributes. The lowest sensory acceptance was recorded in set-yoghurt made from Friesian milk. Thus, milk from TW and LC is likely to be suitable in producing set-yoghurts with superior textural, microstructural and sensory properties, compared to milk from Jersey and Friesian. Our results suggest the merits of using indigenous cow milk in producing set-yoghurts and, thereby, prioritizing the preservation of the genetic pool of these indigenous breeds.