Microalgae biotechnology has made it possible to derive secondary bioactive metabolites from microalgae strains that have opened up their entire potential to uncover a wide range of novel metabolic capabilities and turn these into bio-products for the development of sustainable bio-refineries. Nuclear Magnetic Resonance Technology (NMR) has been one of the most successful and functional research technology over the past two decades to analyse the composition, structure and functionality of distinct metabolites in the different microalgae strains. This technology offers qualitative as well as quantitative knowledge about the endogenous metabolites and lipids of low molecular mass to offer a good picture of the physiological state of biological samples in metabolomics and lipidomics studies. Henceforth, this review is aimed at introducing the metabolomics and lipidomics studies into the field of NMR technology and also highlights the protocols for the isolation and metabolic measurements of metabolites from microalgae that should be redirected to resource recovery and value-added products with a systematic and holistic approach for scalability or sustainability. © 2021 Elsevier Inc.