Microalgae metabolites include biologically active compounds with therapeutic effects such as anticancer, anti-inflammatory and immunomodulation effects. One of the most recent focuses is on utilizing microalgae lipid-based biologically active compounds in food applications. However, most microalgae biological active compounds in their natural forms have common drawbacks like low solubility, low physicochemical stability and strong susceptibility to degradation, which significantly limits their application in foods, therefore, it is important to find solutions to retain their functional properties. In the present work, a comprehensive review on multi-product biorefinery was carried out from upstream processing stage to downstream processing stage, and identify critical processes and factors that impact bioactive material acquisition and retention. Furthermore, since nanoencapsulation technology emerges as an effective solution for microalgae nutraceutical product's retention, this work also focus on the nanoparticle perspective and comprehensively reviews the current nanoencapsulation solutions of the microalgae bioactive extract products. The aim is to depict advances in the formulations of microalage bioactive nanoparticles and provide a critical analysis of the reported nanoparticle formation. Overall, through the investigation of microalgae from biomass to bioactive nanoparticles, we aim to facilitate microalgae nutraceuticals incorporation as high value-added ingredients in more functional food that can improve human health.