This study shows the morphological changes of Saccharomyces cerevisiae EC1118 during the second fermentation of Spanish cava wines, in relation with progression of fermentation and aging. In the first stages of active fermentation, and associated with the increase in viable counts, budding cells and a relative homogeneity in cell size were observed. Close to the moment of sugar exhaustion cells acquired the morphology of stationary phase, to finally enter in a death phase with cell size reduction, and cytoplasm alterations including inhomogeneity, refringency, and detachment of the cell wall. At the beginning of this step structures reminiscent to autophagosomes are observed. This is in accordance with the appearance of molecular markers of autophagy described elsewhere in similar winemaking conditions.