The objective of this research was to evaluate microbiological contamination in the flour and starch during cassava processing in traditional and model units. The total and fecal coliforms indexes, Bacillus cereus, Salmonella, bacteria, yeast and fungi were determined. Bacillus cereus and Salmonella were not detected in any sample. The incidence of microorganisms decreased along the processing to obtain cassava flour, and is lower in model unit. After the roasting process, the microbial load was below the values established by the Brazilian legislation, and can be regarded as a critical step in obtaining cassava flour. Concerning starch production, the microbial load in the traditional units was higher than in the model units, and the increase of the extraction steps has promoted the growth of microorganisms. It's recommended the used of only 4 extractions.