Background and aims: Soil freeze-thaw cycle (FTC) regimes are altered by climate change and known to influence nutrient cycling and plant growth. Here, we explore mechanistic explanations for the changing plant performance of the grass Holcus lanatus and the dwarf shrub Calluna vulgaris. Methods: 120 plant-soil mesocosms were subjected to different FTC-regimes in a climate chamber. Root injury, fungal activity and fungal composition (ITS-sequencing) were quantified. Results: The applied FTC-scenarios increased root injury by 23% on average while no strong differences between scenarios was found. Root damage was greater in C. vulgaris than in H. lanatus. Fungal activity increased due to the FTC-manipulation and was higher in the C. vulgaris samples, although activity was generally low. No significant shift in the fungal community composition was found immediately after the applied FTCs. A saprobic (Aureobasidium pullulans) and a potentially mycorrhizal fungus (Sebacinales) showed opposing responses to the FTC-manipulation in the different host plants, while a potential phytopathogen (Callophora) decreased in frequency. Conclusions: Increased fungal activity within these samples is suggested to be related to an increased dominance of saprobic taxa, but not to a shift in qualitative community composition. Single pathogenic species entering the plants through the observed root injuries subsequent to FTC treatments however, may alter plant performance. While these results suggest the importance of root injury for the response of vegetation to FTCs, fungal activity and pathogenic infection need to be further studied under field conditions over longer time periods.