Crocus sativus L. commonly known as saffron or Kesar in India, is an important medicinal herb in Ayurveda and has been traditionally used for treatment of neurological disorders, for depression, anxiety and sleep disorders. It is uses as a coloring and flavouring agent in the preparation of various foods. Modern research has high lighted its beneficial effects in treatment of cardiovascular action, diabetic cataract, and as a potent antiinflammatory herb. Due to its high cost its quality control is of utmost importance to ensure its authenticity, purity and its medicinal properties. In the preset study the we have used Thin Layer Chromatography (TLC) analysis, High performance thin layer chromatography (HPTLC) fingerprint, UV-Vis spectrophotometric analysis, 1H nuclear magnetic resonance (1H NMR) and Fourier transform infrared spectroscopy (FTIR) based metabolomic study for quality control and characterization of saffron. The antibacterial and antifungal activity were evaluated using agar well-diffusion method in two pathogenic bacterial strains, Escherichia coli, Staphylococcus aureus and two pathogenic fungal strains, Candida albicans, and Aspergillus brasiliensis. The 1H NMR spectroscopy couples with FTIR analysis leads to identifcation of the secondary metabolites of saffron like crocetin, picrocrocin and safranal on basis of reported diagonostic signals and peaks. The antimicrobial activity showed moderate antibacterial and antifungal activity. The TLC and HPTLC profile reveals the characteristic fingerprint. Overall the present study showed that the 1H-NMR, FTIR based metabolomics approach and TLC and HPTLC metabolite profiling can be powerful strategy for maintaining the holistic quality of the saffron.