Mesenchymal Stem Cells (MSCs) are one of the promising cellular therapies for immune-related diseases. Preconditioning of MSCs increases their efficacy and overcomes several hurdles in MSC-based therapies. It reduces tissue inflammation and improves cell survival, consequently enhancing therapeutic outcomes. Evaluating some proteins may elucidate the probable behavior of transplanted cells in cellular therapies. Improving the number of immunomodulatory factors like Programmed cell death ligand 1 (PD-L1), Indoleamine 2,3-dioxygenase (IDO), and Tumor Necrosis Factor (TNF)-Stimulated Gene-6 (TSG-6) could be fundamental to modulate the immune system in immune-related disorders. In the current study, human Bone Marrow-derived clonal MSCs (hBM-cMSCs) were preconditioned with different regimens, especially Interferon-gamma (IFN-γ) to evaluate the effects of these regimens on the desired protein expression patterns to pave the way for clinical applications of MSCs according to their protein production potentials and enhance their therapeutic potential.