The oenological industry has benefited from the use of Nuclear Magnetic Resonance (1H-NMR) spectroscopy in combination with Multivariate Statistical Analysis (MSA) as a foodomics tool for retrieving discriminant features related to geographical origins, grape varieties, and further quality controls. Said omics methods have gained such attention that Intergovernmental Organizations and Control Agencies are currently recommending their massive use amongst countries as quality compliances for tracking standard and degradation parameters, fermentation products, polyphenols, amino acids, geographical origins, appellations d’origine contrôlée and type of monovarietal strains in wines. This study presents, for the first time, a 1H-NMR/MSA profiling of industrial Mexican wines, finding excellent statistical features to discriminate between oenological regions and grape varieties with supervised Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA). In a comparative way, it is applied with the 1H-NMR/OPLS-DA workflow for the first time in ancestral and artisanal Mexican mezcals with promising results to discriminate between regions, agave species and manufacturing processes. The central aim of this comparative study is to extrapolate the know-how of wine-omics into the non-professionalized mezcal industry for establishing the NMR acquisition, preprocessing and statistical analysis basis to implement novel, non-invasive and highly reproducible regional, agave species and manufacturing-quality controls.