Seed consumption has increased in recent years because the high nutrient content of seeds. However, the number of outbreaks caused by Salmonella associated with the consumption of low water activity food items has also increased, although these food items do not support microbial growth. The main goal of this study was to quantify microbial indicators and to determine the prevalence and content of Salmonella spp. in chia, amaranth and sesame seeds obtained from Mexican retail outlets. In addition, the behavior of this pathogen on seeds was also evaluated. One hundred samples of each product (chia, amaranth and sesame seeds) were collected from Queretaro City markets. Aerobic plate count (APC), coliforms and Escherichia coli were quantified, and the presence and number of Salmonella were also determined. Chia, amaranth and sesame seeds (1 kg each) were inoculated with a cocktail containing five Salmonella strains (~6 log CFU mL -1 ) and were stored at ambient temperature and populations of Salmonella were quantified. The median APC contents in chia, amaranth, and sesame seeds were 2.1, 2.4, and 3.8 log CFU g -1 , respectively, and the content of coliforms on the seeds ranged from 0.48 to 0.56 log MPN g -1 . E. coli was present at low concentrations in the three types of seeds. Salmonella was detected in chia (31%), amaranth (15%), and sesame (12%) seeds, and the population ranged from 0.48 to 0.56 Log MPN g -1 . Salmonella spp. decreased through 240 days of storage, showing inactivation rates of 0.017, 0.011 and 0.016 log CFU h -1 in chia, amaranth, and sesame seeds, respectively. The high prevalence of Salmonella in the seeds highlights potential risks for consumers, particularly giving that seeds are generally consumed without treatments guaranteeing pathogen inactivation.