Owing to the declining reserve of fossil resources as well as more concerns on climate change, and essential energy security, and especially the broad consensus on carbon neutralization, it is significantly critical to develop renewable and sustainable energy and chemicals. Algae as alternative resources can be applied to produce biofuels and biochemicals. Among them, algae-derived natural pigments exhibit high market value due to their uses in pharmaceutical and food industries. As a result of the developments of engineering tools, it is feasible to scale up algal processing and applications. Prior to the industrial implementation, life cycle assessment is required to ensure the environmental feasibility of algae-based biofuels and biochemicals. In this article, recent advances in processing algae for liquid, gas, and solid fuels are reviewed. New approaches for enhancing the natural pigment accumulation are also discussed. Recent studies on life cycle assessment of algae-based biofuels and biochemicals, as well as the main challenges faced by the algal biorefinery, are discussed in this manuscript.