Saccharomyces cereyisiae, a eukaryotic model organism, plays a key role in the oxidative stability of fermented products. In order to protect cells against environmental stresses, we report a method of modifying the cell surface architecture while maintaining the internal working properties of the system. The objective was to encapsulate living yeast cells in micro-organized polyelectrolyte shells using layer-by-layer (LbL) assembly. For the first time, the natural polyelectrolytes,beta-lactoglobulin and sodium alginate, were alternately deposited on the surface of S. cerevisiae. Transmission electron microscopy coupled with immune-cytochemistry and scanning electron microscopy provided evidence of the polyelectrolyte layers around yeast cells. The electrostatic interactions between the yeast, beta-lactoglobulin and alginate were assessed using Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR). We observed the preservation of yeast functionality and membrane integrity after encapsulation. Finally, we showed that the LbL method does not influence the yeast growth and improves the yeast viability after freezing treatments in combination or not with chemical (H2O2 or ethanol) stresses. (C) 2015 Elsevier Ltd. All rights reserved.