This study investigates the bacterial-fungal interaction between *Bacillus subtilis* and *Aspergillus niger* using a co-culture experimental evolution approach. The results show that *B. subtilis* adapts to the presence of *A. niger* by increasing its surface spreading ability and production of the lipopeptide surfactin, which inhibits fungal growth and acidification of the environment. Specific mutations in the DegS-DegU two-component system are identified as responsible for these adaptations. Surfactin causes hyphal bulging and cell wall stress in *A. niger*, leading to inhibition of fungal expansion. The study highlights the potential of combining co-culture and laboratory evolution experiments to deepen understanding of bacterial-fungal interactions and their ecological implications.This study investigates the bacterial-fungal interaction between *Bacillus subtilis* and *Aspergillus niger* using a co-culture experimental evolution approach. The results show that *B. subtilis* adapts to the presence of *A. niger* by increasing its surface spreading ability and production of the lipopeptide surfactin, which inhibits fungal growth and acidification of the environment. Specific mutations in the DegS-DegU two-component system are identified as responsible for these adaptations. Surfactin causes hyphal bulging and cell wall stress in *A. niger*, leading to inhibition of fungal expansion. The study highlights the potential of combining co-culture and laboratory evolution experiments to deepen understanding of bacterial-fungal interactions and their ecological implications.