[Objective] To reveal the mechanisms ofPseudomonas putida Y-9 in actively regulating the extracellular and intracellular pH homeostasis during ammonia oxidation.[Methods] Y-9 was cultured in the nitrification media with initial pH 7.19 and 9.40, respectively, for 48 h. Metabolomics was employed to compare the differential metabolites and predict dissociation constant (pKa) during the ammonia oxidation. Transcriptomics was employed to compare the genes regulating.[Results] In the medium with initial pH 7.19, Y-9 produced maltitol to raise extracellular pH, and up-regulated the expression of the genes related to deaminase, deiminase, and cation transport to maintain intracellular pH stability. In the medium with initial pH 9.40, Y-9 produced acidic substances such as 5-aminovaleric acid 3 and oxamic acid to lower extracellular pH and regulated the expression of the genes associated with NADH dehydrogenase, cytochromes, ATP synthase, and amino acid transport to maintain intracellular acidity.[Conclusion] This study revealed the novel phenomenon of Y-9's extracellular pH stabilizing capacity and investigated its intracellular pH homeostasis mechanism. The findings enrich our knowledge about microorganism-environment interactions, and provide a theoretical basis for further understanding the pH stabilization mechanism in microbial denitrification processes.