Background: Food poisoning could be caused by eating the sweets contaminated with microorganisms, which has always been considered as one of the major problems of people in developing countries, including Iran. The aim of this study is to investigate microbial variety and fungal load in the traditional sweets offered in confectionery stores in Yazd province in 2020. Methods: In this study, 170 samples of traditional sweets, referred by confectioneries in Yazd province, were randomly selected and tested for microorganisms contamination such as Enterobacteriaceae, Escherichia coli, Staphylococcus aureus, Salmonella, molds, and yeasts according to Iranian national standards. Results: The highest rate of microbial contamination in samples was related to "Pistachio Loz" (52.94%) and the lowest rate was related to "Hajibadam" (11.76%). The infection rates of Enterobacteriaceae, Escherichia coli, molds, and yeasts were 17.06%, 8.83%, 20.59%, 3.53%, respectively. No infection was observed with Staphylococcus aureus and Salmonella in the samples. Conclusions: Due to the high level of microbial contamination of traditional sweets, especially "Pistachio Loz" offered in Yazd, more control measures are needed in preparation and distribution of such sweets.