This chapter of the book proposes an experimentally feasibly nanojunction in which a quantum dot is integrated in a semiconducting-superconducting heterostructure hosting Majorana bound states (MBSs). The realistic setup we propose could enable the probing of Majorana modes where the energy exchange of the nanodevice with an environmental bath is also taken into account within a single long-wave optical phonon mode. A threading magnetic flux is also considered to manipulate the Majorana-induced phonon-assisted quantum tunneling. The electron-phonon interaction (EPI) is incorporated into the model employing a canonical transformation combined with the nonequilibrium Green’s function technique. The results obtained in this chapter can serve as a promising guide in Majorana detection experiments. Furthermore, the device investigated here is highly relevant to research on the implementation of topological quantum computation.