Sugar beets (Beta vulgaris L.) are grown in temperate regions primarily for sugar production, but also to harness alternative energy. Various pathogens that infect the crop during different life stages are causing diminishing harvests. In order to identify implications of health and disease on the microbiome of field-grown sugar beets an integrative approach was implemented. The antagonistic potential of bacterial isolates from different fields was assessed together with amplicon sequencing libraries obtained with 16S rRNA gene fragments as well as the fungal ITS region. Overall a substantial loss of microbial diversity (bacteriome H’: 8 vs. 6.5 mycobiome H’: 4.5 vs. 3.5) was observed in diseased sugar beets. The Gram-positive Lactobacillales as well as distinct fungal taxa such as Candida, Penicillium and Fusarium were identified as indicators of disease in the microbiome. In contrast, higher microbial diversity as well as distinct taxa such as Vishniacozyma or Plectosphaerella were associated with the microbiome of healthy plants. Along with taxonomic changes varying functions of the fungal microbiome were observed. Pathotrophic and symbiotrophic fungi are replaced by saprotrophic fungi in diseased sugar beets. Moreover, high antagonistic potential within the bacterial community was shown to avert shifts in the fungal microbiome. The findings demonstrate the importance of microbial antagonists and suggest that key taxa are indicative for the health of sugar beet roots. They can be utilized to develop improved disease management systems and to target prevalent pathogens before they can cause disease in the plants.