Is the the peer-review process different for special issues? When I submitted my manuscript for a special issue of IEEE journal 3 months ago, the status of my article was:


  [Administrator]:  [name of publication manager]
  
  Under review


Yesterday it changed to:


  [Administrator]:  [name of publication manager]
  
  Awaiting Recommendation


I am afraid that my article may be desk-rejected because


  [Administrator]:  [name of publication manager]


hasn't changed to


  [Administrator]:  [name of associate editor or editor-in-chief]


Question: Is there any difference in the peer-review process of general submission and submission to a special issue?
Yes, there's a difference in the peer-review process for general submissions and special issue submissions. That's because very often, the special issue involves a guest editor who's not otherwise a member of the editorial board.

In your case I suspect the journal administrator is acting on behalf of the guest editor. That is, the journal did not register an account for the guest editor. The guest editor is still making the decisions, but the journal administrator is inputting those for the guest editor, which is why it appears as though the journal administrator is "awaiting recommendation".

It's unlikely your paper's being desk-rejected. It's been three months. If you do indeed get a desk rejection, that's a black mark against the journal.