<p>How land-use history—particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields—influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including <i>Nitrosocosmicus</i> and <i>Streptomyces</i>, along with enriched genes involved in nitrification (e.g., <i>amoC_B</i>, <i>nxrB</i>) and nitrogen fixation (<i>nifD</i>, <i>nifK</i>), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in <i>Bradyrhizobium</i>, <i>Halobaculum</i>, and <i>Russula</i>, and exhibited higher expression of denitrification-related genes (<i>norB</i>, <i>narJ</i>), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (<i>phoX</i>, <i>glpQ</i>) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.</p>