How do I clean a subfloor so my dog won’t smell past urine spots?

Lots of baking soda, mop with vinegar and water. I'd even use one of the commercial cleaners on market sold at pet stores. Once plywood is dry. Roll on a few coats of oil based polyurethane

I have two small boy dogs. it's a problem for me too. I just mop and spray. don't know how to control this behavior. the go out most of the time through the doggie doors but still have to mark in the house occasionally. let me know if you find an answer.

You would need an enzyme cleaner from the pet store. Natures Miracle is one good brand.

This is not a cleaner it was used for crime scene clean-ups before it was put on residential market. It is an odor neutralizer it works on smell of death,skunk,urine,vomit,feces. Nothing over counter(vinegar,Mother Natures Miracle,Baking Soda etc,)works animals can still smell it even if us humans cannot.It's hard to find & cannot get in concentrate anymore only premixed Sometimes on Amazon https://www.bonanza.com/listings/Pet-Odor-Remover-Stinkers-Odor-Remover-Kills-Odors-Fast-Forever/361143373?goog_pla=1&gpid=76984043821&keyword=&goog_pla=1&pos=1o5&ad_type=pla&gclid=EAIaIQobChMI-v3l2rTQ3gIVFNVkCh3hrwoeEAQYBSABEgJ1kvD_BwE This one with yellow & red label is original