<p>Zinc pollution is a growing environmental concern because of its potential for bioaccumulation and associated toxicity. Microorganisms have attracted considerable interest in environmental governance because of their environmentally benign nature and high efficiency in removing heavy metals. In this study, <i>Stenotrophomonas sepilia</i> FCHC-ZnA2, which has strong Zn-chelating activity, was isolated from highly Zn-polluted soil in China. SEM and TEM analyses showed that <i>S. sepilia</i> FCHC-ZnA2 effectively absorbed Zn²⁺ through extracellular polymeric substances (EPS) on its surface and formed particles. FTIR and XPS analyses confirmed that -SH, C = O, and -OH groups within the EPS matrix effectively enriched free Zn²⁺ and facilitated the formation of insoluble deposits (ZnS) on the bacterial surface. 3D-EEM analysis revealed that Tyr and Trp provided adsorption sites during Zn²⁺ adsorption. Proteomic analysis revealed that under Zn²⁺ stress, <i>S. sepilia</i> FCHC-ZnA2 adapts by enhancing pyruvate metabolism and fatty acid degradation to supply sulfur-containing amino acids while upregulating ribosomal proteins to support EPS synthesis. Subsequently, the downregulation of the MetNIQ transporter suggests a cellular strategy to restrict external sulfur uptake, thereby promoting ZnS nucleation and precipitation.</p> Graphical Abstract <p></p>