Herbs and farm produce are stored after harvest for different durations and have the potential to support microbial growth on them which can lead to shorter shelf life and enhancing food safety issues due to pathogens and allergens. The present study investigated the native microbial loads and aflatoxin contents on Stevia rebaudiana Bertoni leaf samples collected from different cultivar in Odisha during various seasonal harvesting processes. There is a clear indication that the total microbial populations in the leaf samples in the monsoon were significantly higher than summer and winter seasons. Therefore, different measures may be needed to handle and process these samples to minimize food safety risks of the product. Determination of AFB1 levels in stevia leaf samples by enzyme-linked immunosorbent assay (ELISA) procedure revealed that there is consistence presence of aflatoxin AFB1 in all most all samples collected from the region. There was no significant difference in contents within the different types of samples collected. The level of microbial population and aflatoxin contents of all the cultivars irrespective of cultivation cycle or duration needs to be reduced and appropriate post harvest measures needs to be taken for further application of the produce.