Microalgae are increasingly recognized as valuable sources of bioactive compounds with significant prebiotic potential. These photosynthetic microorganisms produce a variety of non-digestible polysaccharides, such as sulfated galactans and β-glucans, which selectively stimulate the growth and activity of beneficial gut microbiota. This chapter explores the structural diversity and functionality of prebiotic compounds derived from microalgae, their mechanisms of action in promoting gastrointestinal health, and the evidence supporting their prebiotic effects. It also highlights the emerging concept of microalgae-based synbiotics, where microalgal prebiotics are combined with specific probiotic strains for synergistic benefits. This chapter further examines the integration of microalgae in functional foods and nutraceuticals, outlines regulatory considerations, and discusses future prospects for their use in gut health and wellness. Overall, microalgae represent a sustainable, multifunctional platform with untapped potential in shaping the future of human nutrition and microbiome-targeted therapies.