Thanks for the further replies. The software is all written on the .net framework, so the core hosting needs to be IIS, although it may be possible to have a layer in front.
@acicali IIS allows you to have multiple sites, but each site is only allowed 1 certificate (Unless you use centralised certificates where it reads from a directory via a naming convention). My current engine runs on a single site so I’m a little stuck there.
As it runs on Azure, it is run a bit like a web farm so I’m currently looking into attaching a shared drive to each of my virtual machines and adding the SSL certificates in there and having IIS run via centralised certificates.
I would then need to try and run a process which generates the new certificates and stores them in the shared folder. There’s going to be a few hurdles to jump through and if any of them causes a block I’ll need another solution, but it will be good if I can get it all working!