The quality and safety of herbal medicines is becoming a major concern worldwide particularly due to contamination by heavy metals. The present study quantified the levels of heavy metals in frequently used South African medicinal plants and determined the variations in certain biological activities and phytochemical compositions. Eleven plant species were obtained from both muthi shops (MS) (commercial outlets) and from open street markets (OSM) for comparison. Samples were dried, powdered and digested using microwave acid-assisted digestion. The digested solutions were analysed for heavy metals using Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). Plants were classified based on their elemental composition using chemometric techniques. Powdered plant samples were extracted using 70% acetone and screened for antibacterial activity against E. coli and S. aureus. Phytochemical analyses were carried out to determine total phenolic and flavonoid content. Of the 22 samples analysed, Bulbine natalensis obtained from OSM and Alepidea amatymbica obtained from MS exhibited high levels of Al [5559 and 4392mg/kg dry weight (DW)] and Fe (4164 and 4465mg/kg DW) respectively. Levels of As and Hg were above the World Health Organization permissible limits in most of the samples analysed. Hierarchical cluster analysis classified the samples into four groups based on their metallic analyte concentrations. Group one having low metal content and group four having a high metal content. In general, plant samples with high levels of metals yielded greater antibacterial activity. However, antibacterial activity recorded in this study is not an indicator of high levels of heavy metal contamination as some samples despite the high levels of metal exhibited low antibacterial activity. The variations in the amounts of phenolics and flavonoids in the evaluated samples could have probably been that some of the plant samples may have been harvested from different localities or at different times of the year, perhaps plant age or degree of storage. The results highlighted the need for in-depth risk and quality assessments