Biological nitrification inhibition is a plant-mediated rhizosphere process where natural nitrification inhibitors can be produced and released by roots to suppress nitrifier activity in soil. Nitrification is one of the critical soil processes in the nitrogen (N) cycle, but unrestricted and rapid nitrification in agricultural systems can result in major losses of N from the plant–soil system (i.e., by NO3− leaching and gaseous N emissions). In this study, we explored the potential efficacy of biological nitrification inhibitors (linoleic acid [LA] and linolenic acid [LN]) and a proven efficient synthetic (dicyandiamide [DCD]) nitrification inhibitor on N dynamics, nitrous oxide (N2O) and carbon dioxide (CO2) emissions in a highly nitrifying soil. 14C-labelled LA, LN and DCD mineralization was determined in a parallel experiment to explore the fate of inhibitors after application. We found that LA and LN had no effect on soil NH4+ concentrations, but significantly decreased NO3− concentrations. Soil that received DCD had lower NO3− and higher NH4+ concentrations than the control (soil without nitrification inhibitors). LA and LN increased the cumulative N2O and CO2 emissions when they were applied at high concentrations (635 or 1,270 mg kg−1 dry soil). LA and LN had a much greater mineralization rate than that of DCD: 47–56%, 37–61% and 2.7–5.5%, respectively, after 38 days incubation. We conclude that in contrast to the direct inhibition of nitrification caused by DCD, addition of LA and LN may cause apparent nitrification inhibition by promoting microbial immobilization of soil NH4+ and/or NO3−. Future studies on nitrification inhibitors need to clearly differentiate between the direct and indirect effects that result from addition of these compounds to soil.