Microbiomes have captured global attention among researchers due to their significant impact on the environment. Microbiomes have captured global attention among researchers due to their significant impact on the environment. Microbiomes have captured global attention among researchers due to their significant impact on the environment. The discovery of microbiomes in fungi adds to this growing interest. Filamentous fungi can house diverse microorganisms within their hyphae. Advanced multi-omics techniques have been employed to study these complex endohyphal microbiomes. However, the full taxonomic and functional diversity of small-scale microbiomes like these remains undiscovered. Conducting integrative multi-omics research is already challenging with large and widely available samples, and small-scale microbiomes further amplify these difficulties. Culturing fungal hosts can be problematic, and small sample sizes complicate library preparation and genome assembly. Nevertheless, studying these "microbiomes within microbiomes" will enhance our understanding of their parent microbiomes. So, researchers must advocate for new tools, methods, and standards to be applied in this rapidly developing field.