How can you fix a car air conditioner that puts out a bad smell for 2-3 minutes when you first turn on the air conditioner?

The AC also removes moisture from the air. The odor problem is probably due to mold caused by a blocked drain hose. Unplug drain hose or replace same.

I start my car; turn the AC to Max, and the air to Recirculate. I then roll down the driver window just enough that I can place a can Lysol through and spray for a few minutes to all the Lysol to work into the AC system. After doing so the car smells great and the annoying initial smell is gone for a few months.

after making sure it will drain properly the best way to permanently remove smells is to use a "ozone machine" or a ionizer this attacks the odor causing molecules and breaks them down. 30-60 minutes from a powerful unit will do the trick , most carpet cleaning companies that also do water repairs have these machines and their rates vary. alpine air also makes a home unit and these are good to use in the home 24/7 as well

Check to see if you have a cabin air filter. For example, new Toyota passenger cars all have them behind the glove compartment. Ask any quick lube or the dealer if you have one.

There is a product that Walmart and auto parts stores sell called Ozium. Follow directions on the can. It kills the bacteria that grows on the condensor of your AC.

On most all vehicles there is a vent just in front of the windshield. Any foregin substance or outside smell (e.g. exhaust gas from the car in front of you) can come into your car through this vent. Turn on fan in your car and pour a mixture of soapy water in the vent outside at the windshield. Some of the soapy water will make it into the fan housing cleaning it. Make sure to run plenty of clean water after to rinse.

I have heard that animals crawl inside the AC box, and make their nests there. I have also heard stories of where squirrels will store store food here (in this case it was dog food). To fix? Pull apart the ducting, clean out whatever smells, and install a cabin filter to prevent little rodents from renetering. If you cannot install a filter, put your air on recirculate when storing the car.