Nitrogen (N) is a vital nutrient essential for both soil microbiota and plant growth. The intersection of climate change and human activities has increased N inputs, leading to notable N losses that have concerning effects on human health. It is widely recognized that soils can retain large amounts of N. Therefore, understanding the global patterns of N cycling, influenced by regional environmental variations, is crucial for estimating soils' N retention abilities. In this paper, we analyzed 2,039 soil metagenomic samples to map out N cycling processes worldwide and revealed significant differences in N cycling among various ecosystems. Remarkably, natural ecosystems, especially grasslands, showed a much higher potential to retain soil N than agricultural lands. Moreover, natural ecosystems provided more consistent predictions of potential N retention relative to total soil N than agricultural systems. This divergence might be due to disruptions caused by intensive farming, which can lead to ecological imbalance in cultivated areas. These insights highlight the urgent need for global sustainable farming practices, aligning agricultural goals with ecosystem health.