Soilborne diseases of cotton such as Verticillium wilt (VW, caused by Verticillium dahliae Kleb, VD) and Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) are a significant threat to cotton quality and productivity and have been identified as key areas for investment by the Australian cotton industry. These cotton diseases have unique characteristics in Australia; therefore, the country cannot rely on disease control approaches developed in different countries/conditions, and a sustainable integrated disease management (IDM) solution tailored to Australian conditions is urgently needed. Plants have developed sophisticated mechanisms to exploit the benefits provided by their co-associated microbes (i.e., the plant/soil microbiome) for disease suppression. Harnessing the functions provided by the plant microbiome can provide an effective approach to sustainably mitigate the impact of soilborne diseases on cotton productivity. This project employed a multidisciplinary approach to contribute to developing a sustainable IDM system to control and predict FW and VW in Australian cotton.