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Mold growth on sausage casing during processing is an important problem in fermented sausages. In this work, sausages were dipped into 1% chitosan (C), 1% thyme essential oil in 1% chitosan (CT), 1% rosemary essential oil in 1% chitosan (CR), 20% potassium sorbate (PS) as chemical antifungal, and 1% acetic acid solution (AA) as chitosan solver, or distilled water (DW) as control after fermentation (at day 4). The changes in microbiological (total viable count, lactic acid bacteria [LAB], Micrococcaceae, Enterobacteriaceae, and mold and yeast counts) and physicochemical attributes of the sausages during 12 days of processing were monitored. As expected, LAB were the most dominant microbiota in fermented sausages and the dipping process did not have any negative effect. Additionally, the treatment with C, CT, and CR suppressed the growth of spoilage microorganisms, which resulted in a significant reduction (P < 0.01) of about 1.4 to 1.6 log CFU/g in Enterobacteriaceae counts at day 12. The C, CT, and CR similarly suppressed the growth of fungi in the interior of the sausages, and the antifungal treatment significantly reduced (P < 0.01) the load of fungi on the casing. Throughout the study, approximately log counts of 3 and 4 in lower molds and yeasts in the casings treated with PS and CR were found, respectively, as compared to DW. Finally, the microbial quality of the end product was notably improved.