Microalgae have been recognized as the foundation of the food chain in aquatic ecosystems and one of the most prominent characteristics of algae is their color, which is determined by their pigments, hence, microalgal biomass is attracting worldwide attention. These pigments are colorful chemical substances that are part of the photosynthetic system of microalgae and are distinguished into three classes: carotenoids, chlorophylls and phycobiliproteins. Besides the color, pigments have health-promoting properties and a broad range of potential industrial applications. Consumers are becoming increasingly aware of the correlation between diet, health, and disease prevention. Despite the beneficial properties of pigments provided by microalgae, their effectiveness at preventing a range of diseases depends on their bioaccessibility and bioavailability. The digestion process comprises several steps, which promotes an intense variation of the conditions that the pigments are exposed, and therefore, could in several ways compromises the health benefits caused by microalgae pigment consumption. Therefore, the present chapter aims to present the main methods used to assess the bioaccessibility and bioavailability of pigments from microalgae to better understand the processes involved. Consequently, providing information about the most accepted analytical protocols in measurement of bioavailability of pigments.