Incorporation of fungal biological control agents (BCAs) into plant growing media has considerable ergonomic and economic benefits for growers. These agents usually give prophylactic control of target pests and diseases. However, their efficacy is dose dependent and loss of inoculum through leaching could influence the degree of protection they provide. At present there are no protocols to determine the loss of inoculum in the disparate growing media used in horticulture. We describe a method based on a nutrient leaching column to quantify leaching of conidia of the insect-pathogenic fungus Metarhizium anisopliae in a range of growing media. Conidia of this biocontrol agent were applied as a drench or premixed into the medium. Both the application method and growth medium influenced conidial leaching. Inoculum losses were greater following drench application than premixing (95% vs. 15%) irrespective of media type. Comparatively more inoculum was lost from bark and coir following drench application whereas losses were relatively high in peat following premixed application. The leaching column assay provided a simple and accurate method to quantify inoculum loss in real time. This assay could help determine leaching of other fungal BCAs in growing media. It could help in improving pest and disease control by optimizing the rate and frequency of conidial application as well in the design of more efficacious formulations.