Aims Plant yield, nitrate accumulation risk, and the potential pathogenic microorganism are critical parameters in evaluating soil fertility management. The nitrate content in the soil–plant system is substantially driven by soil abiotic properties and soil and endophytic microorganisms which are also potential resources of plant pathogenicity. This study aimed to quantify the effects of citric acid (CA), alone or with dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP), on plant yield, nitrate accumulation risk and potential pathogenicity of soil–plant system.

Methods Our study contained six treatments: (1) control without CA or nitrification inhibitor (CK); (2) sole DCD application treatment (DCT); (3) sole DMPP application treatment (DMT); (4) sole CA application treatment (CAT); (5) CA + DCD application treatment (CADCT) and (6) CA + DMPP application treatment (CADMT). The nitrate contents, plant yields, and bacterial communities in soil and plant samples were analyzed.

Results The CA significantly reduced soil nitrate contents by 29.8%. Relative to sole CA application, extra nitrification inhibitor application significantly enhanced plant yields and decreased plant nitrate contents. The exclusive CA application could significantly stimulate the soil Actinobacteriota but reduce the soil pathogenicity, but extra nitrification inhibitors led to higher potential soil pathogenicity.

Conclusions The single CA application could decrease nitrate accumulation risk and mitigating potential soil pathogenicity damage, while extra nitrification inhibitor application would intensify the performances of CA in decreasing plant nitrate accumulation but potentially enhancing the pathogenic. It deserves to emphasize the consideration of the tradeoffs among plant yield, nitrate accumulation risk, and potential pathogen risk when evaluating the effects of CA and nitrification inhibitors.