Carbon (C), nitrogen (N), and phosphorus (P) serve as critical limiting factors for plant-microbe colonization and growth in agroecosystems, while simultaneously functioning as key regulatory controls for soil C emissions. Here, we investigated plant-microbial nutrient limitation under two states of paddy fields (cultivation state and fallow state), assessing synchronization patterns through combined analysis of plant resorption efficiency and microbial ecoenzyme stoichiometry. We found that there was a consistent pattern of N (25.00%) and P (44.44%) limitation between plant-microbial communities. Plant-microbial communities were mainly N-limited in the rice cultivation stage and P-limited in the fallow stage. Nutrient limitation of plant-microbial communities was regulated by soil C:N:P stoichiometry: the increase in available soil N:P led to P limitation in plant communities, which enhanced the secretion of organoheterocyclic compounds and organometallic compounds. This change increased the relative abundance of Chloroflexi and Ascomycota, thereby exacerbating microbial P limitation. Notably, the direct effect of available soil N:P on microbial N:P limitation was as important as the indirect effect through plant communities. The increased available soil C:N exacerbated microbial C limitation primarily through changing microbial composition. Overall, variations in stoichiometry of available soil nutrients drove a transition from N to P limitation in plant-microbial communities during fallow periods. We highlight that fallowing is an important compensatory process to alleviate the C and N limitation of plant-microbial communities resulting from long-term agricultural monoculture patterns.