Natural milk starters, like Italy's lattoinnesto, are rarer than natural whey starters in traditional cheese production, representing a less studied niche. This study aimed to investigate how milk adjunct cultures could enhance microbial diversity, establish a link between terroir and cheese, stabilise production variations, and influence the aroma profile and safety of semi-hard cheeses. Natural milk adjunct cultures were produced from raw and thermised milk by spontaneous fermentation and utilised to produce Vacherin Fribourgeois model cheeses in combination with a commercial starter for acidification. Cheeses produced from raw milk exhibited more diverse flavour profiles and higher concentrations of several volatile compounds than those made from thermised milk. The increased proteolysis in cheeses with enriched lattoinnesto-like adjunct cultures correlated with increased levels of flavour-related compounds and relative abundance of Lactobacillus helveticus. The findings highlight significant differences in microbial composition and flavour profiles based on milk treatment and natural milk adjunct cultures.