Before industrial demolition was common, old buildings would be town down and material repurposed for new constructions, build on top of existing foundations and rubble. Do this enough over the centuries and your city will slowly rise in height.
If anyone’s ever in Barcelona I recommend checking out the history museum, which is literally built on top of some Roman and medieval ruins. You can descend into the basement to see the excavated remains of the foundations of Roman buildings that had been levelled and built on top of.