Lotus (Nelumbo nucifera Gaertn.) is widely utilized in traditional medicine and cuisine throughout Asia, with its leaves containing valuable bioactive alkaloids and flavonoids. However, Lotus leaves are often considered as by-products, urging the need for methods to analyze these components and enhance biological and economic value. In this study, a novel, rapid, and reliable UPLC-MS/MS method was developed to evaluate the quality of Folium Nelumbinis by establishing the first chromatographic fingerprint of simultaneously determination of bioactive alkaloids (nuciferine, O-nornuciferine, N-nornuciferine) and flavonoids (kaempferol, quercetin, isoquercitrin, quercetin-3-O-glucuronide). The method was validated according to the Association of Official Analytical Chemists and European Commission Decision 2021/808/EC guidelines, demonstrating high sensitivity, specificity, and reproducibility, with detection and quantification limits below 0.48 ng/mL and 1.50 ng/mL, respectively. When the procedure was applied to 49 Lotus leaf samples collected across various regions and growth stages in Vietnam, revealing significant regional and developmental variations in alkaloid and flavonoid content. Nuciferine and quercetin-3-O-glucuronide were the most abundant compounds, with the highest alkaloid concentration found in Hanoi and the highest flavonoid content in Lam Dong. Besides, this study contributes not only to the quality control of Lotus leaves but also to the understanding of geographical and developmental impacts on their bioactive composition. The chromatographic fingerprinting initiative described here highlights the application of the approach as a potential standard for the quality and regularity of traditional herbal medicines and hence the sustainable and optimal utilization of Lotus leaves in pharmaceutical and nutraceutical applications.