Early and reliable diagnosis paves the path for effective therapeutic outcomes. Traditional disease diagnosis modalities often fail to satisfy the need. More importantly, several conventional diagnostic tools rely upon the phenotypic manifestation of the disease for its diagnosis, thus causing an inevitable delay in diagnosis resulting in belated therapeutic intervention and poor prognosis. Further, the molecular basis of pathological mechanisms usually remains obscure. Thus, improvements in diagnostic modalities in terms of specificity, sensitivity, resource involvement, potable use for pen-side diagnosis and, most importantly, to facilitate earliest detection is of utmost importance for preferable selection. Biomarker-based disease diagnosis suits the multi-faceted demand to a substantial extent. State-of-the-art proteomics and metabolomics modalities have already contributed immensely in the arena of biomarker discovery for several diseases of human as well as animal subjects. The purview of biomarker-based disease diagnosis is expanding continuously from complex diseases like cancer of human and animal origin to tricky, animal-specific diseases like mastitis. The coverage will certainly increase to include several chronic, metabolic and lifestyle diseases as well as emerging and re-emerging neglected infectious diseases in the near future. Proteins and metabolites, which are the targets of proteomic and metabolomic intervention, respectively, provide nascent information regarding the complex biological networks and aberrations as they are the terminal products of central dogma and metabolic pathways, respectively. Due to penetration up to molecular level, proteomic and metabolomic interventions can elucidate the molecular mechanisms of disease establishment, progression and tentative outcome of a therapeutic regimen implemented against an ailment. Further, they also facilitate the scope of identifying novel therapeutic checkpoints to customize new therapeutics. Drug repurposing is also possible through metabolomics intervention by identifying the common host metabolic pathways exploited by any novel pathogen. Separation-based chromatographic and electrophoretic methods such as liquid or gas chromatography (LC/GC) or capillary electrophoresis (CE) coupled with mass spectrometry (MS), fluorescence-based methods, Raman-based methods, nuclear magnetic resonance (NMR) or direct mass spectrometry imaging (MSI) occupy the bulk of the recent proteomics and metabolomics interventions in disease diagnosis to achieve penetration up to even single-cell level with considerable precision. Persistent developments in sample preparation methods, instrumentation and computational data analyses programs will certainly improve the utility of these cutting-edge platforms toward invention of novel early, reliable and cost-effective point-of-care diagnostic tools for field-level application in animal disease diagnosis.