Treated wastewater (TWW) is increasingly used as an alternative irrigation source to alleviate water scarcity in agriculture; however, its effects on soil microbial communities and potential microbial contamination remain a concern. This study evaluated the chemical and microbial quality of TWW for irrigation and its effects on selected soil chemical properties and microbial communities using tomato (Solanum lycopersicum) as a test crop. A 90-day greenhouse pot experiment was conducted using two tomato cultivars (Roma and Rodade), irrigated with TWW from four wastewater treatment plants (Bochum, Polokwane, Mankweng, and Lebowakgomo), with tap water serving as the control. Soil samples collected at crop maturity were analysed for pH (water and potassium chloride), electrical conductivity (EC), beneficial microorganisms (Actinomycetes, Pseudomonas putida, and phosphate-solubilising bacteria), pathogenic bacteria (Escherichia coli, Salmonella, Staphylococcus, Shigella, Vibrio cholerae, Enteric bacteria, and Pseudomonas aeruginosa), and total bacterial and fungal counts. Irrigation water source was the main factor influencing soil chemical and biological properties, while tomato cultivar effects were negligible. Compared with the pre-irrigation soil, TWW irrigation increased soil EC by 109%–528% and soil pH by 24.5%–41.6%, whereas tap water reduced EC by 68.9%. Beneficial microbial populations increased under TWW irrigation, with Actinomycetes, P. putida, and phosphate-solubilising bacteria increasing by 131%–136%, 117%–124%, and 88%–96%, respectively. Total fungal and bacterial populations increased by up to 195.5% and 131.7%, respectively. However, TWW irrigation also elevated populations of several pathogenic bacteria, with E. coli, enteric bacteria, Salmonella, and Staphylococcus increasing by up to 72%, 141%, 73%, and 75%, respectively. In irrigation water, pathogen concentrations frequently exceeded the FAO and WHO guideline of 1,000 CFU/100 mL for unrestricted irrigation. Overall, TWW enhanced soil microbial activity and beneficial microorganisms, demonstrating its potential as a sustainable irrigation source in water-scarce regions. Nevertheless, routine monitoring and improved wastewater treatment are required to minimise pathogen transfer and support safe agricultural reuse practices.