Topological insulators (TI) are a class of materials gaining in importance due to their unique spin/electronic properties, which may allow for the generation of quasiparticles and electronic states which are not accessible in classical condensed-matter systems. Not surprisingly, TI are considered as promising materials for multiple applications in next generation electronic or spintronic devices, as well as for applications in energy conversion, such as thermo-electrics. In this study, we examined the practical challenges associated with the formation of a well-defined junction between a model 3D topological insulator, Bi2Te3, and a metal, Fe or Eu, from which spin injection could potentially be realized. The properties of multilayer systems grown by molecular beam epitaxy (MBE), with Fe or Eu thin films sandwiched between two Bi2Te3 layers, were studied in-situ using electron diffraction and photoelectron spectroscopy. Their magnetic properties were measured using a SQUID magnetometer, while the in-depth chemical structure was assessed using secondary ion mass spectroscopy. An examination of impact of Bi2Te3 structure on chemical stability of the junction area has been realized. For Fe, we found that despite room temperature growth, a reaction between the Fe film and Bi2Te3 takes place, leading to the formation of FeTe and also the precipitation of metallic Bi. For the Eu tri-layer, a reaction also occurs, but the Te chemical state remains intact.