Phyllanthus amarus (Schum. and Thonn) has been used traditionally for treating over 50 diseases globally including malaria in Tororo, Uganda. Although efficacy and acute toxicity studies of this plant have been determined, safety regarding microbiological analysis and total aflatoxins levels in this Ugandan shoot powder of P. amarus is still lacking. The microbiological analysis was determined according to the procedures recommended in WHO guidelines. Total aflatoxins were determined using Afla Test Kit, VICAM Series (South Africa). In terms of microbial analysis, the herbs were prepared based on indigenous knowledge according to the WHO criteria. Although this herbal shoot powder had microbial safety requirements with key microbial contaminants (i.e. mold fungi, Salmonella typhi, and Escherichia coli) within acceptable ranges, however, aflatoxins in all the investigated samples were beyond acceptable levels. Current results are useful in developing and establishing public health standards for the production and safe handling of herbal products of the Ugandan P. amarus.