Phenolic compounds constitute probably the largest group of plant secondary metabolites and have key roles in plant metabolism. Simulated nitrogen (N) deposition is important to agriculture and has considerable impacts on plant phenolic metabolism but a systematic understanding of such effects is lacking. We here synthesized results from 123 articles and evaluated the responses of plant biomass, in vivo N status, soluble sugar concentrations, carbon (C)/N ratios and multiple phenolic compounds to the simulated N deposition. This meta-analysis showed that the simulated N deposition significantly increased plant biomass and N content but reduced the concentrations of phenolic compounds in a dose-depended manner. This was linked to the suppression of phenolic generating phenylalanine ammonia_lyase activity and key associated gene expression by the simulated N deposition. Total phenolic concentrations were negatively related to biomass but were positively correlated with C/N and soluble sugar contents. Overall, our results indicated adverse effects of simulated N deposition on phenolic metabolism which could compromise key aspects of crop quality and are apparently hidden by positive effects on plant biomass. Our findings have significant ecological and biological implications for plant phenolic metabolism facing global N deposition.