Protein sequestration plays an essential role in maintaining stem cell populations in the native stem cell niche. Both pluripotent and adult stem cells require the sustained presentation of numerous bioactive growth factors and other soluble cues to potentiate cell fate decisions and morphogenic events. Consequently, methods of natural protein sequestration employed by the stem cell niche present attractive strategies for developing novel protein delivery vehicles and engineering biomimetic stem cell microenvironments that enhance morphogen bioactivity. In this review, we will explore the role of protein sequestration in the native stem cell niche and how it has inspired the design of several classes of materials that exploit natural protein sequestration to effectively maintain stem cell populations and direct stem cell fate. We will also highlight several recent developments in protein sequestering biomaterials, in which material strategies to sequester complex mixtures of endogenously secreted proteins are also being investigated.