ABSTRACT Available soil nitrogen (Av-N) is an important indicator for understanding the soil fertility in paddy fields. Previous studies have reported a decline in Av-N resulting from paddy-upland rotation at a regional scale in Japan, while the factors influencing this phenomenon on a national scale are not well understood. This study aims to assess the effects of soil temperature, land use, soil type and soil texture on Av-N in paddy fields across Japan. Soil surveys were conducted in 13 prefectures in 2020 and 2021, involving the collection of soil samples from the plow layer in a total of 2,600 paddy fields. Our results revealed that soil temperature had the most significant influence on Av-N, followed by land use and soil type. Av-N exhibited a negative correlation with soil temperature, whereby the average Av-N in the thermic soil temperature regime (>15°C, Av-N: 107 ± 48 mg kg−1) significantly lower than that in the mesic soil temperature regime (≤15°C, Av-N: 166 ± 74 mg kg−1). Increased upland frequency in paddy fields led to a decrease in Av-N, particularly pronounced in the thermic soil temperature regime, while partially mitigated in the mesic soil temperature regime. In the thermic soil temperature regime, paddy fields with long-term upland usage (upland frequency of paddy fields was more than 50%) had an average Av-N of 50 mg kg−1, necessitating additional organic matter application. Furthermore, the results concerning soil type and soil texture indicated that Av-N was higher in wet soil compared to semi-wet soil, and fine-textured soil had higher Av-N than medium-course textured soil. These findings underscore the negative effect of accelerated drying in paddy fields due to the expanding practice of paddy-upland rotation, leading to decreased Av-N. In conclusion, our study proposes the importance of organic matter management practices, with a primary emphasis on soil temperature, further refined by considering land use and soil type, to ensure the maintenance of adequate Av-N levels in paddy fields in Japan.