I was moving some stuff around in my garden and I found an old stump. The Salvia I was moving was right next to it. As I was digging up the Salvia I noticed a stench. Smelled like raw sewage. Roots of this stump don't look very healthy and only had one tiny leaf growing from it. Is it root rot?

It is a musty odor coming from the decomposing stump. Perfectly natural.

Hmmm... do you have a septic tank? Is your soil waterlogged?

I'm a bit puzzled by an old stump that has a leaf growing from it. If it's not a septic problem as Daisy suggested, the only other thing that comes to mind is that the still living "stump" is a plant that is dying of bacterial soft rot, which is well-known for a very strong and disgusting smell.

As a stump decomposes over time, a great number of plants take hold in the decaying wood. You would see more things out in the forest but this is probably why he has something living in his stump.

No septic near the garden. So if it's decomposing it's no good any more, right? Thinking about pulling it out...

P.S. the smell went through my gloves. Washed my hands five times and the odor is still there. So gross!

If it is decomposing to the point of an odor being emitted, nothing will ever come from it.
I think that you might be better served by just letting it continue the way it has been going. The odor will subside because basically there was no odor until you disturbed the stump.
You could break it apart with tools a dispose of the pieces but that's going to be messy. Could you cover the stump with soil? That might hasten it's breakdown.

You're probably right about leaving it be. The odor will probably be even worse if I dig it up and expose more of the rot.

Thanks everyone!

In the future, if you get something that leaves an odor on your hands, pour a little salt on your wet hands & "wash" with the salt, then rinse. Smell should be gone.

@purpleinopp, rubbing alcohol finally got rid of it.

Awesome! Happy to suggest.