The type, functions, and mechanisms of biological nitrification inhibitors (BNIs) from rice were investigated using a combination of chemical and molecular techniques, bacterial bioassays, and soil microcosm experiments. We report the discovery of an effective nitrification inhibitor, syringic acid, in the root exudates of rice. Nitrification inhibition activity by syringic acid was verified in both weakly acidic and neutral pure cultures of Nitrosomonas europaea, and was superior to the widely used synthetic nitrification inhibitor, dicyandiamide (DCD). Moreover, syringic acid exhibited a dual inhibitory effect on ammonia monooxygenase (AMO), active in ammonium/ammonia oxidation, and on urease, active in urea hydrolysis. Nitrification inhibition by syringic acid was also demonstrated in a paddy soil system, and the abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was significantly inhibited under all syringic acid treatments. A synergistic effect of syringic acid and another rice BNI, 1,9-decanediol, on nitrification was found in two pure Nitrosomonas cultures and a paddy soil. Together, our results enhance our understanding of BNI production by rice and enable the design of natural inhibitor formulations that regulate soil N transformation in a concerted manner.