An integrated circuit packaging system and method of manufacture thereof including: providing a substrate; forming contact pads on top of the substrate; forming a protection layer on top of the contact pads and the substrate; exposing the contact pads from the protection layer; printing under bump metallization (UBM) layers over the exposed contact pads extended over the protection layer with conductive inks; and forming bumps on top of the under bump metallization layers. It also including: printing an adhesion layer using conductive ink, wherein the adhesion layer comprises interconnected adhesion layer pads; forming additional under bump metallization (UBM) layers and bumps on top of the adhesion layer pads utilizing an electro-deposition process; and removing connections among the interconnected adhesion layer pads.