Microalgae are found across a diverse range of environments, each endowed with a unique metabolic profile. They offer a potential platform to produce valuable products on account of their adaptability, high growth rate, and simple nutritional requirements. Further, coupled with their natural ability to sequester CO2 into biomolecules, microalgae have gained significant attention as a sustainable microfactory. However, the genetic traits for unique metabolite production in algae often fail to generate sufficient quantities. Hence, efforts have been made to improve the quantity, quality, and scalability of value-added products via media engineering and genetic interventions. This chapter particularly outlines recent advances in the metabolic engineering of algae, focusing on genetic tools employed to enhance metabolite yields and successful strain improvement. Key genome editing tools discussed include CRISPR-Cas, RNA interference (RNAi), and overexpression/heterogeneous expression strategies with endogenous and heterologous promoters. Case studies highlight the engineering of algae for enhanced production of valuable compounds, such as lipids (e.g., DHA, EPA), carotenoids (e.g., astaxanthin, β-carotene), and other high-value metabolites like polyunsaturated fatty acids (PUFAs). These examples showcase the potential of genetic manipulation to redirect metabolic flux, improve pathway efficiency, and ultimately increase the titer, rate, and yield of desired products. This chapter also discusses the challenges in developing robust tools applicable to a wider range of algal species. Future directions involve refining existing genetic tools and integrating systems biology approaches to enable a more precise and predictable metabolic engineering approach for the industrial-scale production of valuable compounds from algal cell factories.