Microalgae are a promising feedstock source for third-generation biofuels. However, applying microalgae as a raw feedstock for biodiesel production presents several challenges regarding its economic feasibility, particularly during the harvesting stage. The microalgal harvesting stage is crucial from an economic perspective, and it impacts the feedstock quality during subsequent downstream processing steps. The factors of microalgae fatty acid profile (FAP) and lipid yield (LY) are subject to variability throughout the harvesting process. Successful harvesting relies on the application of strategies that provide optimal performance without imposing any qualitative or quantitative reduction in FAP and LY (FAP&LY). Although the promotion of the harvesting efficiency of microalgae has been studied extensively, little is known about how the harvesting process impacts FAP&LY, and even less is known about how it influences the lipid extraction process. This paper provides a compendium of technical developments intended to promote FAP&LY during the harvesting process. In this study, the importance of pre-harvesting, harvesting, and post-harvesting strategies for enhancing the FAP&LY is discussed. It was shown that co-cultivation specific microalgae with fungi, bacteria, or other microalgae strains could improve the flocculation efficiency and FAP&LY. Algae-algae co-cultivation had higher FAP quality compared to others. Appropriate wet storage conditions and stress induction strategies could promote the FAP&LY efficiency and reduce the expenses incurred by cell drying and associated instruments. Enhancing FAP&LY via the harvesting process could be exploited as breakthrough technology for cost-efficient microalgaebased biodiesel production.