Sugar loss due to storage rot is still an economically important factor in the sugar industry. The colonization of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps represents a challenge for postharvest technology. Colonizing bacteria were found to play a key role in controlling the introduction of fungal pathogens in several plant models. To observe the interplay of bacteriome and myobiome in sugar beet after harvest, cultivation dependent methods were compared to molecular methods to obtain a detailed picture of the bacterial and fungal community colonizing sugar beet roots. Comparison of beets from several beet clamps in Austria and Germany highlighted regional taxonomic differences, however universal signs of health status. Significant differences (p= 0.01) between healthy and diseased sugar beets were observed, relying on a decreased microbial diversity (healthy sugar beets H’= 5.5 (bacteriome) and 4.5 (mycobiome) vs. diseased sugar beets: H’ 4.5 (bacteriome) and 3.5 (mycobiome)) as well as changed taxonomic composition. Fungal taxa such as Candida and Penicillium and gram-positive bacterial taxa such as Lactobacillales were indicators for a diseased microbiome. On the other hand, genera such as Plectospaerella and Vishniacozyma as well as higher microbial diversity in general were found to indicate a more healthy and stable microbiome. The knowledge generated in this study can be used to improve current and next-generation postharvest management techniques.