Summary Many plant‐associated fungi host endosymbiotic endobacteria with reduced genomes. While endobacteria play important roles in these tri‐partite plant–fungal–endobacterial systems, the active physiology of fungal endobacteria has not been characterized extensively by systems biology approaches. Here, we use integrated proteomics and metabolomics to characterize the relationship between the endobacterium Mycoavidus sp. an...