1. Plant-associated microbial communities are crucial for plant growth and play an important role in disease suppression. Community composition and function change upon pathogen attack, yet to date we do not know if these changes are a side effect of the infection or actively driven by the plant. 2. Here we used a split-root approach to test whether barley plants recruit bacteria carrying antifungal traits upon infestation with Fusarium graminearum. Split-root systems allow disentangling local infection effects, such as root damage, from systemic, plant-driven effects on microbiome functionality. We assessed the recruitment of fluorescent pseudomonads, a taxon correlated with disease suppression, and of two well-described antifungal genes (phlD coding for 2,4-DAPG and hcnAB coding for HCN). 3. We show an enrichment of fluorescent pseudomonads, phlD and hcnAB upon pathogen infection. This effect was only measurable in the uninfected root compartment. We link these effects to an increased chemotaxis of pseudomonads towards exudates of infected plants. 4. Synthesis. We conclude that barley plants selectively recruited bacteria carrying antifungal traits upon pathogen attack and that the pathogen application locally interfered with this process. By disentangling these two effects we set the base for enhancing strategies unravelling how pathogens and plant hosts jointly shape microbiome functionality.