KNOTTED-LIKE HOMEOBOX (KNOX) proteins are homeodomain containing transcription factors, and regulate many aspects of plant development through homo or heterodimerization with another group of TALE transcription factors known as BELL. In Medicago truncatula the MtKNOX3 gene is involved in nodule development. In this work, we hypothesized that MtKNOX3 involvement in the activation of cytokinin signaling during nodule development could be through heterodimerization with BELL proteins. Thereby, the expression of different BELL genes in Medicago was analyzed, and it was shown that the expression of Medtr8g078480 and Medtr8g098815 genes increases during nodule development. Besides, the Medtr8g078480 shows a co-expression pattern with MtKNOX3 at different developmental stages of nodule development. Afterward, the interaction of MtKNOX3 with the MtBELL1-2 (Medtr8g078480) protein was shown using docking, and their stability was analyzed by molecular dynamic simulation and mmpbsa methods. Moreover, the stability of MtKNOX3- Medtr8g078480 heterodimers was compared with the MtKNOX3 homodimer.