- When I got in, there were four people in the room, besides me.
- When I got in, there were four people in the room, except me.
Are both examples above saying that there are five people?
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I won't say they are used interchangeably in your sentence. Although "except" means "excluding / not including", its usage here is not suitable as you seem to exclude yourself from the group of people who are in the room rather than including yourself in the counting or not.
"Besides" usage is correct. It means "in addition to", and the count will be five as a total (including you).
But in either choice, the comma shouldn't be presented.
When I got in, there were four people in the room besides me.
If you want an alternative for "except", I suggest you use "other than":
When I got in, there were four people in the room other than me.
And the count here will also be five (including you).