Atomic force microscopy (AFM) has now become a major technology to study single cells in living conditions. It provides nanoscale resolution imaging capacities and is a sensitive force machine able to record piconewton-scale forces, thereby making it possible to gain insights into the nanomechanical properties and molecular interactions of cells. While an extensive number of studies on microorganisms have demonstrated the potential of AFM to understand complex phenomena at cell's interfaces, its use in microalgae studies remains limited. These recent years, microalgae have been the subject of a significant number of fundamental studies notably because of their capacity to convert light, water and inorganic nutrients into a biomass resource rich in value-added products. The existing literature reporting AFM use to understand microalgae cell morphology, their nanomechanical properties or their interactions with their environment give a large overview of the contribution AFM can bring into microalgae studies. In this review, we will first present the principles of AFM and the different possibilities it offers to characterize cells. Then in a second part, the contribution of AFM to understand the effects of environmental conditions and external stress on microalgae cells will be discussed. Finally, we will show how AFM can be used to probe the interactions of microalgae with their environment and how such fundamental studies can represent a basis to improve microalgae production systems. Overall, this review, the first on this topic, aims to highlight the opportunities that AFM technology can bring to this field of research.