The return of plant residues to the soil is used to promote soil carbon sequestration, improve soil structure, reduce evaporation, and help to fix carbon dioxide in the soil. Microbial communities colonize plant residues during decomposition is expected to be highly dynamic with diverse ecological functions. We aimed to characterize microbial communities colonizing wheat straw residues and their ecological functions during the early phase of decomposition. The experiment was conducted in conventional farming system under both ambient conditions and a future climate scenario expected in 50–70 years from now. We used MiSeq illumina sequencing and network analysis of bacterial 16S rRNA and fungal ITS genes. Our results showed that future climate alters the dynamics of bacterial and fungal communities. We detected various microbial ecological functions within wheat straw residues such as plant growth promoting bacteria, N-fixing bacteria, saprotrophs and plant pathogens. Interestingly, plant pathogenic fungi dominated (~87% of the total sequences) within the wheat residue mycobiome under both ambient and future climate conditions. Therefore, we applied co-occurrence network analysis to predict potential impacts of climate change on the interaction between pathogenic community and other bacterial and fungal microbiomes. The network of ambient climate consisted of 91 nodes and 129 correlations (edges). The highest number of connections was between the pathogen Mycosphaerella tassiana and Plectosphaerella oratosquillae with other microbes while the network of future climate consisted of 100 nodes and 170 correlations. The highest number of connections was between the pathogen Pseudopithomyces rosae and Gibellulopsis piscis with other microbes.