I hate to tell you this, but sometimes the only solution is pulling up the carpet and replacing the subfloor. I bought a house years ago with a similar issue that resulted in having to do exactly that.

We had the same problem when we moved into our house. The upstairs bathroom had a urine smell no matter how much cleaning we did. The floor was linoleum. When we pulled it up to put down tile, we discovered the wooden sub floor had been saturated with urine. We had to rip it all up and replace it, which solved the problem.

Pull the carpets and check the subfloor.

Check the crawl space for things.

Ozone machine might help.

We had this happen and it wasn’t a urine smell - but a dank rotten smell. Turns out a galvanized pipe in the crawl space had corrosion and was leaking kitchen sink wastewater into the dirt crawl space.

Rotting wood can sometimes emit a pretty gross urine smell. Either that or animal urine soaked through the carpet into the subfloor. The only fix for that is to replace the subfloor, or maybe seal it with special paint. But if you’re going to tear up the carpet anyway you might as well replace the subfloor than risk the paint not working and having to do it all over again.

We found the problem wasn’t the floor, it was the crawlspace. Previous owners had removed a screen to the crawlspace and it seems every stray cat in the neighborhood used it as a latrine and the not-quite-dead rodents they dragged in had done the same (and screwed up the insulation).

Had been found in the inspection, so the project wasn’t a surprise. But we didn’t notice the cat pee smell in the bedroom until we got the keys. Happily, it went away after we had contractors resolve you crawlspace mess.

I suggest maybe checking from the bottom up. Go into the crawl space and see what you can see. Or smell. Or both. Just make sure to get PPE from Home Depot because crawlspaces can be some of the nastiest places on Earth.

If you’re not up to it then see if you can find a local company that would inspect for you. Usually a home inspector, a foundation company that does crawlspace encapsulation, or even a handyman if you can find one you really trust to recognize an issue and honestly report back.

ETA: Also, check the vents. When I was a kid I remember someone had a little brother that was a sleepwalker who would sometimes pee in the vents in his sleep.

Subfloor soaked up piss. Then they put new carpet over it.

Real solution is seal the subfloor. But that’s expensive. Consider deploying an ozone machine a few times. It will bet better in time but probably always be there some.

It’s in the crawl space based on the 2 rooms with direct access

check the crawlspace first. if it smells strong down there, you know it’s not the carpet.

Rat piss. I have two locations where eats get under my house and in the summer you can smell it coming through. The heat makes it smell worse.

Start with a small ozone generator if your state or country allows it. They work wonders, and they don’t cost a lot when compared with contractors, carpet layers, etc.

An ozone generator may help. Don’t be home while you use it. May need to run it weekly for a while. They use ozone to get rid of smells from fire and dead things.

Ozone generator after a thorough inspection and cleaning or replacing the damaged stuff. Also Kilz paint on all walls. After all that have an inspection and cleaning of the furnace and ductwork.

Do you have a light fixture in the rooms? The ceramic used for the bulb sockets can break down and give off a urine smell when the light is on and heating up the ceramic.

the fact that it’s only the two rooms with crawlspace openings is a big clue imo. i’d tape plastic over the floor hole in the furnace closet and the access door for a couple days and see if the smell drops. if it does you know it’s coming from the crawl and not the carpet, and then it’s a pest or crawlspace company you call, not a flooring guy.

Urine trouble…

It’s probably urine.

Saturate the subfloor with a pet enzyme cleaner.

Odoban works really well, too. And it’s cheap!

The subfloor and the pad under the carpet

Maybe someone peed in the ductwork.

How’s the crawl space smell?

Enzyme cleaners deal with protein odours and are great for urine or pet messes.

I have a tree or shrub outside my bedroom window that smells like pee. Real bummer when the window is open!

Cat urine? Subfloor definitely needs to be checked, perhaps even replaced along with the floor.

New carpet can be pulled up and reinstalled easy.

Likely the subfloor. I bought a property with this issue. I painted the affected subfloor with kilz oil primer 2 coats. It worked.

Also smell the heat vents. Maybe a cat or kid pissed in them.

Check for mold in the crawlspace, some mold can smell like pee

My was saturated concrete slab fron parrots. Had to hot water and TSP the real tsp, and mopped 2 times rinsed 2 time still smelled. Got kilz which has sel and painted twice.

Close any inside to crawl space. U need to going crawl space and investigate.