Besides the involvement in the pathogenesis of type 1 diabetes mellitus (T1DM), IFNγ is used to license mesenchymal stem cells (MSCs) for displaying immunomodulatory properties. Therefore, we aimed to investigate the interaction of MSCs in two preconditioned (IFNγ⁺) and non-preconditioned (IFNγ⁻) conditions, with PBMCs from healthy control (HC) and T1DM sources in the co-culture system and hypothesized differential induction of chemokines and their receptors, and T regulatory (Treg) cells due to the function of IFNγ. Our results confirmed that MSC/IFNγ⁺ and MSC/IFNγ⁻ treatments reciprocally respond to cell contact with HC and T1DM PBMCs differently, regarding the expression of anti-inflammatory genes (IDO1, IDO2, ICAM-1), chemokine ligands (CCL3, CXCL9, CXCL10) and receptors involved in immune cell trafficking(CXCR3, CXCR6, TLR4). Our results also demonstrated significant differences between HC and T1DM PBMCs by interaction with AF-MSCs (in IFNγ⁺ and IFNγ⁻ states) through paracrine and cell contact approaches regarding the expression of some target genes, including CXCR3 and its ligands (CXCL9 and CXCL10), CXCR6, CCR5and its ligands (CCL3 and CCL4). These differences were also reflected in the proportion of Treg cells in HC and T1DM samples. Therefore, the presence of regulatory roles of IFNγ in the pathogenesis of autoimmune diabetes seems inevitable.