Protagonist saves the world by killing monsters by transforming into different mecha using disks
A few potential options, some of these are a shot in the dark hoping some of your information is mixed up:


Monster Rancher - Monsters were born from disks and used to battle other monsters. Not a mecha anime and came out in 1999. Protagonist doesn't transform most of the time.
Saint Seiya - Has transforming protagonists that look mecha-like. I don't recall any disks though, it came out in the late 80s.
Escaflowne - Came out in the 90s, mecha like.


It could also be some flavor of Digimon, Gundam, etc.

Very few Mecha anime that weren't Gundam or Macross came out in the 90s that I'm aware of; but here is a list.