Why Does My Chihuahua's Ears Stink. They Also Drain Clear Fluid. I Have Treated For Ear Mites, But This Problem Still Occurs. My Puppy Is 3.5 Months Old. He Also Often Shakes His Head And Scratches His Ears.?

Ear mites are not the only cause of stinky itchy ears in dogs. Infection caused by yeast or bacteria causes discharge, pain, inflammation, and smell. Your vet will examine your dog's ears with an otoscope, and take samples to examine under the microscope to determine what kind of agent is responsible. Your dog will need antibacterial or antifungal eardrops to clear the infection, and your vet may also administer some pain relief. Ear infection is a very painful and uncomfortable condition. Left untreated the infection can spread to the middle and inner ear and cause permanent damage. In addition, head shaking can lead to aural haematoma. This is a condition caused by haemorrhaging of blood vessels in the ears. I would urge you to contact your vet and give your dog some relief.

Sounds like a yeast problem to me. My pit bull has the same symptoms, caused by an allergy to wheat. Every spring it gets worse.  I clean his ears with a deodorizing/drying solution I get at the vet for about 11 dollars. He also gets a steroid shot to keep it under control. On occasion I give him a benadryl per the vets instruction.

Food allergies!!! I didn't know that when my dog was a few weeks old. I learned the hard way. He now, several years down the road, has serious seizures due to food allergies. Do not feed your dog commercial dog food. Beef and chicken are on top of the list. Research dog food.
Best of luck,
Yianna