Durable resistance against fungal pathogens is highly valuable for disease management in agriculture. For its sustainable use, and to avoid pathogen adaptation, it is important to understand the underlying molecular mechanisms. Many studies on durable disease resistance in plants have focused exclusively on the host plant, whereas possible reactions and adaptations of pathogens exposed to this type of resistance have not been well researched. The wheat Lr34 gene, encoding a putative ABC‐transporter, provides broad‐spectrum and durable resistance against multiple fungal pathogens in wheat and is functional as a transgene in all major cereals. Lr34‐based resistance is partial, meaning pathogens can grow and reproduce to some degree on Lr34‐containing plants. Therefore, Lr34‐expressing plants are ideal for studying the response of pathogens to partial resistance. Here, transcriptomic responses of the two fungal pathogens Blumeria graminis f. sp. hordei (barley powdery mildew) and Puccinia triticina (wheat leaf rust) during growth on their respective host plants containing Lr34 were compared to their responses on control plants without Lr34. Two different time points after inoculation were chosen for analysis of powdery mildew on barley and one time point for wheat leaf rust. Transcriptome analyses revealed that there were no differences in the expression patterns of the two pathogens growing on susceptible versus partially resistant plants, even though pathogen growth was reduced in the presence of Lr34. This reflects the absence of observable reaction in the pathogen to the presence of the Lr34 resistance gene and, consequently, no major alteration of fungal pathogen metabolism.