Here we report the results of a study of the formation and functioning of AM in processing tomato farm soils from across southeastern Australia. In a survey, which included the majority of processing tomato producers in the industry, mycorrhizal colonization of roots was generally low, and in many instances, completely absent. This result can be explained by the use of soil fumigants on many farms. While previous cropping history did not explain levels of AM colonization, the proportion of mycorrhizal crops in the rotation had an influence on soil C, which was generally low across most sites. In an effort to further explore the functioning of AM, a targeted glasshouse experiment was undertaken, in which a mycorrhiza defective tomato mutant and its mycorrhizal wild-type progenitor were grown under uniform conditions. While AM colonization of plants was highest when grown in soil collected from an un-farmed site in this glasshouse experiment, AM provided a greater benefit (in terms of root Zn nutrition) when grown in soil collected from more fertile farm sites. Together, these data indicate that farm management decisions (in this case soil fumigation) may have consequences for the formation of AM, which in turn, may reduce the benefits of AM in these farm soils.