Shilajit (Mumijo) is a phytomineral exudate known for its therapeutic potential, traditionally used in Ayurvedic medicine. Its molecular composition and consequently its therapeutic properties are influenced by geographical origin. Low-field nuclear magnetic resonance (LF NMR) offers a non-destructive tool to assess the molecular behavior of Shilajit rapidly and non-destructively. Twelve raw Shilajit samples from five regions (Iran, India, Nepal, Russia, and Kyrgyzstan) were analyzed using LF NMR at 15 MHz. Longitudinal magnetization relaxation (T1) and transverse magnetization relaxation (T2) relaxation times were measured using an inversion-recovery and Carr–Purcell– Meiboom–Gill pulse sequence, respectively. Three distinct relaxation behavior groups were identified. Group I showed only T1 (solid samples with undetectable T2), group II exhibited single T1 and T2 (moderately viscous, hydrated samples), while group III revealed biphasic T2 relaxation (indicating proton heterogeneity). Clear differences in relaxation profiles were observed across geographical origins, with Iranian samples showing the widest range of T1 values, while Russian and some Iranian samples exhibited dual T2 components. LF NMR relaxation parameters (T1, T2) are strongly dependent on the geographic origin and molecular structure of Shilajit. The technique shows promise for use in authentication and traceability of Shilajit, enabling differentiation based on relaxation signatures.