A method of protecting through substrate via (TSV) die from bonding damage includes providing a substrate including a plurality of TSV die having a topside including active circuitry, a bottomside, and a plurality of TSVs that include an inner metal core that reaches from the topside to protruding TSV tips that extend out from the bottomside. A protective layer is formed on or applied to the bottomside of the TSV die including between and over the protruding TSV tips. The TSV die is bonded with its topside down onto a workpiece having a workpiece surface and its bottomside up and in contact with a bond head. The protective layer reduces damage from the bonding process including warpage of the TSV die by preventing the bond head from making direct contact to the protruding TSV tips.