<title>Abstract</title> Aims Maize/soybean intercropping has many advantages in soil nitrogen (N) use compared with monocultures. However, whether fungi increase the mineralization of soil organic N in intercropping remains unknown. We hypothesized that the fungal-mediated N mineralization in intercropping increases soil mineral N. Methods Soil was sampled in a 13-year field experiment with monocultured maize, monocultured soybean and maize/soybean intercropping without N input (N0) and with 180 kg N ha<sup>− 1</sup> input (N180). The net N mineralization, N mineralization-related enzymes (urease and protease) and fungal communities were analyzed to show whether N mineralization occurred and the role of fungi in N mineralization. Results Based on the long-term experiment, the redundancy analysis showed that the soil chemical properties and enzyme activities explained 67.92% of the total variation of fungal communities. Intercropping increased the net mineral N content by 1.6 times compared to monocultured maize, mainly due to the increase in net ammonium content, the richness and diversity of fungal communities were not affected by intercropping under N0. There is no correlation between the net mineral N content and the relative abundance of fungal communities in different crop systems, but the net mineral N content was increased with the relative abundance of Glomeromycota under N180 (<italic>p</italic> = 0.04). Conclusion Maize/soybean intercropping increased the net N mineralization without affecting the soil fungal communities under no N input. The increased relative abundance of Glomeromycota under N input has potential to increase net N mineralization regardless of crop systems. This study provides evidence of N mineralization driven by intercropping under no N input. However, further research is needed to explore the microbial mechanism of N mineralization.
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