The biological control of plant pests with beneficial microbes has become increasingly important over the last decades. Root colonising fungi can promote the growth of plants and often trigger a weak plant defence response. This weak induction, called priming, enhances the immune response of the plant at subsequent pathogen attacks and increases the resistance to other invaders. While biocontrol agents are applied against a variety of plant pests, fundamental knowledge of the molecular mechanisms of these plant-microbe interactions is still lacking. The fungal biocontrol agent Acremonium alternatum controls mildew fungi and also affects the development of the clubroot pathogen Plasmodiophora brassicae within Arabidopsis thaliana and Brassica roots. Clubroot is a devastating disease in crop plants such as cabbage and rapeseed and causes abnormal root growth that leads to so-called “clubroots”. Co-inoculation of clubroot plants with the fungus A. alternatum reduces clubroot symptoms in Chinese cabbage, rapeseed and Arabidopsis. Overall the endophyte A. alternatum is a very promising candidate for the use in integrative pest management in plant strengtheners or as biocontrol agent.