Microalgae are recognised as a promising source of high-value nutraceuticals such as pigments (carotenoids, tocopherols, etc.), polyunsaturated fatty acids (EPA, DHA), polysaccharides, and proteins. Despite extensive research on the identification of potential species for various value-added products, commercial production of microalgae is still in its infancy. Still, a number of challenges need to be addressed for developing economically feasible and sustainable microalgal biorefinery. Holistic life cycle analysis studies on microalgal biomass production and conversion to value-added products is an urgent requirement. Life cycle analysis helps to identify the hotspots of the process by providing the environmental footprint. It needs to be integrated with life cycle costing and socio-economic analysis in interpreting the sustainability of the microalgal biorefinery process. In this chapter, reports in the literature on life cycle analysis for the production of bioactive compounds from microalgae have been summarised, and a life cycle analysis case study describing the need for developing efficient cultivation processes is discussed.