Biological interactions often involve the transport of molecules, ions, or other species across biological membranes or between interacting proteins. The understanding of these transport phenomena is crucial for the development of therapies for various diseases. Atomic force microscopy is a powerful tool that has been increasingly used to study biological systems at the nano scale. The high resolution, quantitative measurements, and the ability to probe biological interactions under near-physiological conditions make AFM an attractive tool for investigating transport phenomena in biological systems. In this article, we focus on the use of AFM in the study of the transport phenomena in biological systems. We discuss the principles of AFM, its instrumentation, and its application in the study of biomolecules and biological systems. We also provide a comprehensive overview of recent articles that have utilized AFM in the study of biomarkers in biological systems.