Microalgae are a source of a wide variety of commodities, including particularly valuable pigments. The typical pigments present in microalgae are the chlorophylls, carotenoids, and phycobiliproteins. However, other types of pigments, of the family of water-soluble polyphenols, usually encountered in terrestrial plants, have been recently reported in microalgae. Among such microalgal polyphenols, many flavonoids have a yellowish hue, and are used as natural textile dyes. Besides being used as natural colorants, for example in the food or cosmetic industry, microalgal pigments also possess many bioactive properties, making them functional as nutraceutical or pharmaceutical agents. Each type of pigment, with its own chemical structure, fulfills particular biological functions. Considering both eukaryotes and prokaryotes, some species within the four most promising microalgae groups (Cyanobacteria, Rhodophyta, Chlorophyta and Heterokontophyta) are distinguished by their high contents of specific added-value pigments. To further enhance microalgae pigment contents during autotrophic cultivation, a review is made of the main related strategies adopted during the last decade, including light adjustments (quantity and quality, and the duration of the photoperiod cycle), and regard to mineral medium characteristics (salinity, nutrients concentrations, presence of inductive chemicals). In contrast to what is usually observed for growth-related pigments, accumulation of non-photosynthetic pigments (polyphenols and secondary carotenoids) requires particularly stressful conditions. Finally, pigment enrichment is also made possible with two new cutting-edge technologies, via the application of metallic nanoparticles or magnetic fields.