Historic Rebel (HR) cheese is an Italian heritage cheese, produced from raw milk during the summer grazing period in the Alps. The aim of this work was i) to characterize the cheese microbiota, by 16S rRNA gene amplicons sequencing and the volatile and non-volatile lipophilic fraction, by Gas Chromatography and Dynamic Headspace - Extraction Gas Chromatography- Mass Spectrometry, and ii) to evaluate their respective associations. HR cheese was dominated by Firmicutes phylum (99% of the entire abundance), with members of the Streptococcus, Lactobacillus, Lactococcus, Leuconostoc and Pediococcus together representing 87.2% - 99.6% of the total abundance. The polyunsaturated fatty acids composition showed a high PUFA n-3, PUFA n-6 and CLA content, two fold higher than typical plain cheeses. A complex volatilome was detected, dominated in terms of abundance by ketones, fatty acids and alcohols. The main terpenes compounds were α-pinene, camphene and β-pinene.The HR cheese showed a great diversity (P<0.05) of bacterial species and lipophilic fractions among producers, despite they belonging to a small alpine area, revealing a scarce cheese standardization and a chemical fingerprint of a typical mountain cheese produced during the grazing period. A deeper knowledge of the variability of HR cheese will be appreciated in particular by elite consumers looking for niche products, adding economic value to farming in these alpine areas.