Stress conditions and antifungal drugs induce significant changes in the cell wall composition of yeasts and fungi. They cause modifications of the cell wall molecular architecture, including nature, repartition and attachment of cell wall proteins to the cell surface. Atomic Force Microscopy (AFM) is a powerful tool for studying the morphology, nanomechanical and adhesive properties of live microorganisms under physiological conditions. We imaged and measured the biophysical consequences of various stresses on both S. cerevisiae and C. albicans cell morphology at the nanoscale, focusing on changes in cell surface aspect and characteristics: roughness, elasticity, and adhesive properties. AFM allowed us to unravel the morphologic effect on yeast cells of Heat Shock, Osmotic Shock, exposure to toxins and drugs. Moreover, using Single Molecule Force Spectroscopy (SMFS) we can now explore the organization of adhesins, map them on the cell surface and quantify their adhesion forces. Altogether, our studies establish the great interest of AFM to explore molecular mechanisms occurring on the cell surface of live fungal cells.