Abstract: Quantitative Nuclear Magnetic Resonance (qNMR) stands as a selective, accurate, and prompt method for quantitative analysis, predominantly employed in purity assessments of organic compounds. Its potential as a primary method has generated burgeoning interest and applications in international metrological comparisons. The recent international metrological development strategy plans to extend its conventional scope from hydrogen spectroscopy (¹H) to fluorine and phosphorus spectroscopy. The incorporation of qNMR in new domains such as metabolomics, environmental analysis, and physiological research has introduced more intricate molecules and systems, like natural products, biomolecules, proteins, and metabolites, thereby challenging the standard ¹H-qNMR. This has led to an increased focus on qNMR methodologies based on other NMR-active nuclei such as fluorine (¹⁹F) and phosphorus (³¹P). These methodologies offer comparable sensitivity, enhanced resolution, and the ability to eliminate interference from residual solvents or water peaks relative to ¹H-qNMR. This review presents the distinctive advantages, methodological enhancements, and the latest research developments in ¹⁹F-qNMR and ³¹P-qNMR. Particular emphasis is placed on the development of traceable reference materials, coaxial internal standard insertion methods, and parameter optimization. The application domains of ¹⁹F-qNMR encompass medicine, materials, and environmental sciences, whereas ³¹P-qNMR is centered around food, medicine, and biological sectors.ound food, medicine, and biological sectors.