In Metro Manila, the Skyway passes over the following existing overpasses/bridges:
- EDSA crossing over SLEX at the Magallanes Interchange
- Buendia Flyover (Osmena Highway) in Makati
- pedestrian bridge over the San Juan River in Punta, Santa Ana
- Bacood-Mandaluyong Bridge
- Sevilla Bridge
- San Juan Bridge
- LRT-2 transit viaduct
- EDSA overpass over A. Bonifacio Avenue/NLEX at the Balintawak cloverleaf + LRT-1 transit viaduct
- Camachile Flyover and Old Novaliches Flyover (NLEX semi-directional Y interchange with Quirino Highway near Balintawak)