Through billions of years of evolution, nature has been able to create highly sophisticated and ordered structures in living systems, including cells, cellular components and viruses. The formation of these structures involves nucleation and self-assembly, which are fundamental physical processes associated with the formation of any ordered structure. It is important to understand how biogenic materials self-assemble into functional and highly ordered structures in order to determine the mechanisms of biological systems, as well as design and produce new classes of materials which are inspired by nature but equipped with better physiochemical properties for our purposes. An ideal tool for the study of nucleation and self-assembly is in situ atomic force microscopy (AFM), which has been widely used in this field and further developed for different applications in recent years. The main aim of this work is to review the latest contributions that have been reported on studies of nucleation and self-assembly of biogenic and bio-inspired materials using in situ AFM. We will address this topic by introducing the background of AFM, and discussing recent in situ AFM studies on nucleation and self-assembly of soft biogenic, soft bioinspired and hard materials.