As a natural inhabitant of gastrointestinal tract, Lactobacillus plantarum is well known for its health-promoting effects, especially in heavy metal-removal function. The response mechanism integrated physiology and proteomics of Lactobacillus plantarum under excessive manganese stress was systematically performed. More extracellular polymeric substance was secreted, whereas cells preferred to aggregate for resisting manganese stress. The stability of the membrane was maintained by up-regulating the proportion of unsaturated fatty acids, especially cyclopropane fatty acids. The contents of intracellular Asp and Arg, closely related with energy metabolism, decreased under excessive manganese stress. Comparative 2-DE proteomic analysis identified 52 proteins that significantly differed under different levels of manganese stress. The differentially expressed proteins, involved in the carbohydrate, amino acid, stress response and nucleotide metabolisms, were categorized as the crucial components during resisting manganese stress. Moreover, MntH 4 and MntH 5 were identified as the functional elements in regulation of manganese transportation model. The differential expression of six key transporter proteins under different manganese stresses indicated that the MntH 1, 2 and 3 was negatively regulated by MntR, while the regulation of MntH 4 and 5 presented the contrary model. Taken altogether, the study provides new insights into the response mechanism of probiotics to similar environmental stress.