We report multi-channel electron transport in nano-contacts fabricated using focused electron beam induced deposited (FEBID) cobalt and focused ion beam induced deposited (FIBID) tungsten. Anomalous Andreev reflection (AR) effect is observed to which the conventional Blonder–Tinkham–Klapwijk (BTK) fit cannot be applied. In specific, we have observed multiple number of shoulders near the AR peak, whose origin is unknown in literature. We explain this effect based on a simple model that takes into account the material properties of the FIBID grown W superconductor, as well as the specific interface properties that are an outcome of using FEBID/FIBID as a fabrication technique. We show that numerical calculations using the BTK approximation based on the consideration of multiple channels generate similar shoulders as we observed in the AR experiments. Electrical measurements and x-ray photoemission spectroscopy carried out on FIBID W deposits puts additional evidence towards multi-channel current transport occuring at the interface of the nanocontacts.