Hyundai Santa Fe AC smells bad – causes and diagnosis

If the AC in your Hyundai Santa Fe smells like a pile of dirty socks, it could be due to unwanted bacteria growth like mold or mildew. Inhaling these unpleasant musty odors is not only irritating, breathing the airborne microscopic mold spores can cause allergic reactions in sensitive individuals; such as sneezing, runny nose, red eyes, nausea, and skin rash.

Hyundai Santa Fe
Hyundai Santa Fe – (Jan Kliment / Shutterstock)

The most common causes for bad AC smell in Hyundai Santa Fe are dirty cabin air filter, dirty or moldy evaporator coil, clogged condensate drain, and mold growth in the air ducts. In rare cases, bad smell from the air vents can also be caused by rodent infestation.

1. Clogged cabin air filter

Dirty AC filter is one of the leading causes of bad smell coming from air vents in Hyundai Santa Fe. The pollen filter, also known as the cabin air filter or microfilter, is responsible for filtering the air that the passengers breathe in the cabin. A dirty filter causes the overall ventilation of the interior to deteriorate resulting in reduced cooling and poor airflow. If the cabin air filter has not been replaced for a long time, it can get clogged and harbor mold growth, especially in humid environment.

There is no prescribed time for changing cabin air filter, but most manufacturers recommend a change after 10,000-20,000 miles. If you drive your vehicle in dusty or polluted environment, the filter can get dirty much sooner than manufacturer’s recommendation.

Can you clean a dirty cabin air filter?

Instead of changing the cabin air filter in Santa Fe, it is often recommended to first clean the filter. This can be done, for example, with a vacuum cleaner or a compressed air system, removing at least a large part of the visible dirt particles. Unfortunately, this procedure does not allow you to get into the deeper layers of the filter. Therefore, the filter performance will not increase significantly even after cleaning. As a rule, there is no avoiding a change if the filter is dirty or has mold growth on it.

Recommended video

2. Dirty evaporator

If the AC in your Santa Fe smells like dirty gym socks, dirty evaporator coil could be the reason. The cabin air filter captures most of the dirt and other airborne particles, but some particles escape and can get lodged on to the evaporator. Over time, these particles build up on the fins and impede the airflow through the evaporator coil, causing poor airflow from AC vents and degraded cooling performance.

When you turn on the air conditioning system in your Santa Fe, moisture develops along the evaporator coil and then drips down into a condensate drain pan, which then drips under the vehicle. If the evaporator coil is dirty, the layer of dirt and grime on the fins absorbs the moisture and becomes a breeding ground for mold growth.

Dirty vs clean AC evaporator coil comparison.

Symptoms of a dirty evaporator

The two most prominent symptoms of a clogged up evaporator in Santa Fe are: the air flow from the AC vents is choppy and not smooth, and the inside of the vehicle is developing a bad moldy smell.

Clean the evaporator

Cleaning the evaporator in Santa Fe is not a simple task. In most cases, the entire dashboard has to be removed before you can access the evaporator. Therefore, it is recommended to do this in a workshop.

3. Clogged evaporator drain

If the condensate drain under the evaporator coil is clogged or is not draining properly, it not only becomes perfect breeding ground for mold growth, but can also cause water to leak on the floorboard of your Hyundai Santa Fe.

Symptoms of clogged drain

If the moisture/water is accumulating in the condensate pan due to clogged drain, you may hear a sloshing water sound coming from behind the dashboard and is especially noticeable when making turns.

How to unclog the drain

The easiest method to unclog a condensate drain in Santa Fe is by using compressed air. Locate the evaporator drain tube under your vehicle and blow compressed air into the tube hole. Dirty moldy water may gush out as soon as you blow in compressed air, so wear safety glasses and keep your face away from under the drain tube.

If you don’t have compressed air, you can try unclogging the drain by inserting a flexible wire into the tube hole. Give it a good wiggle to loosen up any caked-in dirt and grime in the drain.

4. Dirty air ducts

The air ducts in the air conditioning system of your Santa Fe guides the air from the blower motor to the AC vents. They can get dirty over time and become susceptible to mold growth under humid climate conditions, causing musty smell when the AC is in operation.

There are AC disinfectant sprays available in the market that you either spray directly into the vents in the dashboard, or spray into the fresh air intake vent at the bottom of the windshield.

5. Rodent infestation

If your Santa Fe AC smells like urine and feces, its possible a rodent like a mouse has made its new home in the AC ducts.

A mouse nest in AC blower motor cage.

Inspect the AC system in your Santa Fe for any signs of rodent nesting. Remove the blower motor from under the passenger side dashboard. Get yourself some safety glasses and a medical mask and look up into the ducting for any additional debris. Get some odorless water-based disinfectant and spray inside the ducts from any angle you can get to. Rodents can carry gravely serious pathogens that can go airborne from their feces (e.g. hantavirus), so you should not take a risk with this, especially if you have children in the vehicle.

6. Stinky engine compartment

It is possible that the foul odor coming from the AC vents of your Santa Fe is actually from the engine compartment. Any bad odor in the engine compartment can travel through the air conditioning system and make its way into the cabin even when air-circulation is enabled. This is because the air conditioning system is designed to allow up to approximately 10 percent of the air coming from the air vents to be fresh air from the outside.

Inspect the engine compartment of your Santa Fe for any foul odor. Rodents are known to make home in engine compartments and sometimes get caught up in the moving parts. If that is the case, the rotting stench from the decomposing rodent should be apparent when you open the hood.


There are many reasons why your Hyundai Santa Fe AC has bad smell. When looking for the reason, you should always start with the most obvious causes, dirty cabin air filter or evaporator coil.

In any case, it is advisable for laypersons to visit a workshop. A professional mechanic can swiftly diagnose the bad ac smell issue for you.

Author: Nabeel K