Alginate is one of the mostly used hydrogels for cell entrapment aimed for applications in food industry, environmental engineering, pharmacy and biomedicine. One of the major parameters affecting cell viability and activity is cell distribution inside the immobilization matrix. In addition, changes in cell distribution over the cultivation time could indicate mass transfer limitations, favorable local environments or cell differentiation. In this study, immobilization and distribution of brewing yeast in alginate microbeads were investigated as a model system of colony forming cell growth. Cell distributions were attained by image analysis of histological cross-sections of microbeads used in beer fermentation. A mathematical model based on cellular automata approach was developed for three-dimensional simulations of cell arrangement over the fermentation time.