Rheumatoid arthritis (RA) causes inflammatory and metabolic imbalances in tissue, which then exacerbates inflammation in affected joints. Therefore, restoring tissue homeostasis is necessary for the remission of RA symptoms. In fact, the changes in immunological and metabolic tissue homeostasis at different stages of the disease is not well understood. Herein, the changes in the immunological metabolic profiles in different stages of RA namely, early, intermediate, and late stage was examined. Moreover, the efficacy of the microparticle inverse‐vaccine, paKG(PFK15+bc2) to restore immunological and metabolic tissue homeostasis at different stages of the disease was also investigated. Analysis of the immune cell profiles revealed that there was a significant decrease in the activation of pro‐inflammatory immune cells while a remarkable increase was seen in regulatory T‐cell populations in the intermediate and late stages of RA in the inverse‐vaccine treated group as compared to no treatment. Also, it was determined that glycolysis in the spleen was normalized in the late stages of CIA, which was similar to no disease tissues. Using metabolomics we identified, key metabolites UDP‐glucuronic acid and L‐Glutathione oxidized that were significantly altered between treatment groups, and thus might provide new druggable targets for RA. We also employed flux metabolic modeling of the metabolomics data to identify amino acid and carnitine pathways as the central pathways affected at the tissue‐level in CIA as the disease progresses. Overall, this study shows that the inverse‐vaccines initiate early re‐establishment of homeostasis and persists through the disease span.This article is protected by copyright. All rights reserved