The pathogen Fusarium oxysporum formae specialis cubense (FOC) has caused devastating economic losses in banana production systems. An improved understanding of how agronomic practices can affect the soil microbiome and related agro-ecosystem services, such as disease suppression, may assist in reducing impacts of FOC. This is the first study to investigate whether suppression of FOC, due to use of ground cover management in cultivation of Ducasse banana, is associated with changes in the soil microbiome. A field experiment was undertaken at a site where commercial production of Ducasse bananas had ceased due to Fusarium wilt (indicating high soil inoculum levels). Suppression of Fusarium wilt tended to increase with time in Ducasse bananas cultivated with ground covers compared to bare soil (the vegetated and bare treatments respectively). Terminal restriction fragment length polymorphism (TRFLP) and amplicon sequencing were used to profile microbial communities in bulk soils during the course of the field experiment. TRFLP analysis identified statistically significant changes in the structure of soil microbial communities over time in the vegetated treatment and identified potential bio-markers related to disease suppression. Fungal amplicon sequencing confirmed the findings of TRFLP, and demonstrated reduced dominance of FO in the vegetated treatment was associated with disease suppression. Limitations of using the ITS region for FO/FOC analysis were also determined. The results of this study provide an improved understanding of the mechanisms involved in suppression of FOC by use of ground covers in cultivation of Ducasse bananas, which may be useful for other agricultural production systems.