A multi-layer interconnect structure with a self-aligning barrier structure and a method for fabricating the same is disclosed. For example, the method includes forming a via through an interlayer dielectric (ILD) layer, an etch stop layer (ESL), and a contact structure, pre-cleaning the via with a metal halide, forming a barrier structure on the contact structure in-situ during the pre-cleaning of the via with the metal halide, and depositing a second metal in the via on top of the barrier structure.