A first metal layer can be deposited over first dielectric material layers of a first substrate, and can be patterned into first bonding pads. A first low-k material layer can be formed over the first bonding pads. The first low-k material layer includes a low-k dielectric material such as a MOF dielectric material or organosilicate glass. A second semiconductor die including second bonding pads can be provided. The first bonding pads are bonded to the second bonding pads to form a bonded assembly.