Among plant disease management strategies, biological control is a sustainable alternative to the use of chemicals for the control of vascular wilt caused by Fusarium oxysporum. Fusarium wilt is the most devastating disease affecting a wide variety of plants. Bacillus species are the most widely used biological control candidates for the control of these fungal diseases. This review describes the pathogenicity of F. oxysporum, its virulence mechanisms, and host plant–pathogen interactions. The control means deployed by Bacillus species inhibit or kill these phytopathogens. Bacillus spp. produce a wide range of secondary metabolites, including volatile and non-volatile organic compounds. Biocontrol potential is achieved through direct antimicrobial activity, the induction of the host plant’s immune response (Induced Systemic Resistance), and competition for nutrients and space. In addition, parameters governing the selection of effective biocontrol agents and their survival in plant microbial communities are discussed. The influence of the microbiota on the establishment and development of biocontrol agents can assess the potential of these treatments and facilitate the development of effective biopesticides during their field application.