Wheat take-all is a root disease which devastates crop yields, caused by the ascomycete fungus Gaeumannomyces tritici. The closely related root endophyte, G. hyphopodioides, has been found to induce local host defence responses which confer protection against take-all and reduce disease severity. Chancellor et al. (2024) investigated host transcriptional response to early colonisation by each of these two fungi. Using this RNA-seq dataset in conjunction with newly available Gaeumannomyces reference genomes, we have completed the picture by characterising the fungal transcriptional activity underpinning these different lifestyles. Even at early time points, their transcriptional profiles differ: G. hyphopodioides shows signs of transcriptional reprogramming between 4 and 5 days post inoculation (dpi), mirroring the wheat response, whereas G. tritici expression varied very little between these two time points despite progressing into the vasculature, instead exhibiting a stealthy expression profile dominated by gene downregulation at earlier time points. Moreover, GO term enrichment in this study identified a stress-response unique to G. hyphopodioides, which may explain the formation of its subepidermal vesicles (SEVs), putative resting structures that are a key difference between the pathogen and non-pathogen, alongside upregulation of many putative effectors and CAZymes. The enrichment of a key lignin-degrading CAZyme may contribute to the lack of stress-response identified in G. tritici, allowing fungal hyphae to overcome localised host lignification. These findings highlight the transcriptional basis of colonisation differences and are a step towards understanding how closely related fungi with different lifestyles modulate their interactions within a common host and