The reclamation of domestic wastewater for irrigation is one alternative approach to solve the water scarcity crisis, but it is essential to control the microbiological quality of wastewater used for irrigation. The removal of thermotolerant coliforms, also known as faecal coliforms (FC), from treated domestic wastewater by intermittent media infiltration (IMI) in column was studied. The columns were filled with natural filter media (soil, soil/charcoal and zinc-modified zeolite, Zeo-Zn), and wastewater, IMI-treated wastewater and disinfected wastewater were compared. The numbers of residual FC on Swiss chard (Beta vulgaris) and in agricultural soil were determined over a 4-month period. The column using Zeo-Zn had a higher FC removal efficiency (2.98 log) than columns with other filter media and disinfection (1.87–2.57 log) due to the bactericidal properties of Zn2+. The treatment of wastewater using Zeo-Zn and disinfection both decreased the accumulation of FC on plants and in soil to approximately 1–20 MPN/g dry matter. IMI-treated wastewater using the column with Zeo-Zn was suitable for unrestricted agricultural use, complied with Mexican regulations (as did disinfected wastewater) and had a low risk of FC contamination of plants and soil.