In this work, two levels of addition of microparticulated whey protein (MWP) and whey protein concentrate 35% (WPC35) were used for designing semi-skim (∼1.1 g 100 g−1), high-protein yoghurts (≥7 g 100 g−1). Acidification rate, gel formation, carbohydrates, organic acids, volatile compounds, structural and textural aspects, physicochemical and microbial composition, were assessed. Differences were detected in gel formation by Optigraph® (onset of gelation occurred at lower pH for yoghurts with MWP), but similar fermentation times were observed in every case. Higher firmness, consistency and apparent viscosity were found for yoghurts with WPC35, but some lumps were seen when using the highest level of addition. CLSM images revealed different patterns that may support structural differences; also, ingredient's particle size observed by SEM were correlated with the ordering of the protein network. Relevant flavour compounds, like acetaldehyde, acetoin, and diacetyl, were higher in yoghurts with MWP, while ketones predominated in yoghurts with WPC35.