Is Stale Barn Air Making Your Horse Cough? How to Find Out and Fix It

Last updated: October 15, 2026

By: Miles HenryFact Checked

A horse that coughs every time he comes in from the paddock is telling you something about the air in your barn. If yours coughs in the stall but breathes fine outside, or you catch a sharp whiff of ammonia when you open the barn in the morning, you’re probably wondering what’s in that air and what you can do about it.

Below, I’ll cover what pollutes barn air, how to control ammonia and dust at the source, what your floors have to do with it, how to check your barn’s air, and which fixes make the biggest difference in a barn you already have.

What Affects Horse Barn Air Quality?

Barn air picks up contaminants from almost everything that happens in a stall. According to a University of Illinois veterinary presentation on barn air quality, barn dust comes mainly from hay, bedding, and manure, and it carries bacteria, molds, endotoxin, and mites. Dust is highest near the ground and rises when stalls are cleaned. Add ammonia from urine, and a closed-up barn can hold a lot of irritants right where horses breathe.

That matters because a horse moves a huge volume of air, especially when he’s working. Dust and ammonia irritate the airways and can lead to a chronic cough, poor performance, and respiratory disease. They’re especially hard on horses with heaves, a condition now often called severe equine asthma. A cough that improves outside and worsens in the barn is a strong clue that the environment is part of the problem, but a lingering cough always deserves a call to your vet to rule out infection.

Ammonia: Where It Comes From and How to Control It

Ammonia comes from urine. According to a University of Tennessee Extension study of ammonia in horse stalls, the urea in urine and manure is quickly converted to ammonia by an enzyme found in many plants and microorganisms. Ammonia is released where urine soaks into bedding, mats, and flooring, so readings are often highest near the floor. That’s where horses lie down and eat, and foals spend more time there than anyone. In that study, floor-level ammonia near urine spots in straw-bedded stalls topped 800 ppm in some locations.

The University of Illinois material identifies around 10 ppm as a level where ammonia can irritate the airways, and the federal workplace limit for people is 35 ppm over 15 minutes. Researchers don’t know the exact level that harms horses, so the goal is simply to keep it as low as you can. Here’s how:

• Pick out wet spots every day. Remove urine-soaked bedding and manure daily, or twice a day if you can, and strip stalls on a regular schedule.
• Use absorbent bedding. In the Tennessee study, shavings averaged lower ammonia than straw.
• Use a stall product made for ammonia. Zeolite-based products and stall acidifiers bind or neutralize ammonia at the source when sprinkled on wet spots.
• Skip the ground limestone. The Tennessee researchers warn it’s alkaline, which actually encourages ammonia to form and escape.
• Don’t overfeed protein. Extra protein is excreted as urea in urine. Feed to meet your horse’s needs, not well beyond them.
• Take the horse out while you clean. Stripping wet bedding releases a burst of ammonia and dust, so clean while your horse is turned out or tied outside.

Dust and Mold: Hay, Bedding, and Cleaning

Hay is the biggest dust source in most barns. Purdue Extension’s guide to dust management recommends storing hay as far from the stalls as possible, ideally in a separate building, and never directly over the stalls, where it becomes a constant source of dust and mold spores. When a load of hay arrives, open a few random bales and check them for dust and mold before you stack it.

For horses that cough, the Illinois material also recommends feeding good-quality hay, wetting or soaking it, or switching to hay pellets or cubes, and avoiding round bales for stalled horses.

Bedding is another major dust source. The Illinois material notes that straw produces about three times more dust than shavings. Whatever you use, choose a product that’s absorbent and as dust-free as you can find, and compare your options when you’re deciding on the best type of bedding for a horse stall.

How you clean matters, too. Dry-sweeping an aisle while horses are standing in their stalls puts dust right back into the air they’re breathing. Sweep or blow out aisles when the horses are turned out, and lightly dampen dusty aisles before you sweep.

Floors, Mats, and Drainage

Your floor decides where the urine goes. Dirt and clay floors soak up urine, which keeps feeding ammonia into the stall no matter how well you pick out the bedding. Urine that seeps under stall mats or through the seams between them does the same thing. The Horse reported ammonia readings of 450 ppm under the mats in some high-end show barns.

• Use seamless or interlocking mats and seal the edges so urine can’t pool underneath.
• Lift and clean under mats periodically if they aren’t sealed, and let the floor dry before putting them back.
• Make sure stalls drain or slope so urine doesn’t puddle in one spot.

If you’re building or redoing stalls, compare the flooring for stalls and aisles and the pros and cons of concrete stall floors with mats on top.

How Ventilation Helps Barn Air Quality

Ventilation carries stale air out and brings fresh air through the barn, but it can’t fix every air quality problem on its own. It works best alongside clean bedding, dry stalls, careful hay storage, and regular manure removal. Penn State Extension recommends about 4 to 8 air changes per hour in a horse barn, though the right rate depends on the barn, the season, and the ventilation design, and the Illinois material recommends keeping humidity below 70 percent. Getting the eave vents, ridge vents, stall windows, and fans right is what good horse barn ventilation is all about.

How to Check Your Barn’s Air

You don’t need a lab to know whether your barn’s air needs work. Here’s what to check:

• Smell it when you first walk in. Your nose gets used to ammonia after a few minutes in the barn, so pay attention to the first breath when you open up in the morning, before stalls are cleaned.
• Check down low. Ammonia and dust readings are often highest near the floor, so crouch down in a stall to get a horse’s-eye view of what he’s breathing when he lies down.
• Look for dust in the light. Dust hanging in a beam of sunlight through a stall door or window is a sign the hay, bedding, or cleaning routine needs attention.
• Look for condensation. Moisture on walls, windows, or the underside of the roof means the barn is holding too much humidity.
• Measure if you want numbers. Handheld ammonia meters and test strips give you actual readings, and an inexpensive hygrometer tells you whether humidity is staying below 70 percent.

Improving Air Quality in an Existing Barn

Most air quality problems can be fixed without rebuilding. In an existing barn, start with the sources:

• Choose lower-dust bedding and keep stalls dry.
• Remove wet bedding and urine spots promptly, every day if you can.
• Store hay away from the stalls, in a separate building if possible, and never directly overhead.
• Feed clean hay, and wet, soak, or switch to cubes for horses that cough.
• Fix the floors with sealed or interlocking mats and better drainage so urine doesn’t soak in or pool.
• Avoid dry-sweeping around horses, and dampen dusty aisles first.

If the stalls still feel stuffy after you’ve dealt with the sources, the next step is improving airflow in an existing barn, from opening up the eaves to adding stall windows and fans.

Clean air in a barn doesn’t come from one big fix. It comes from a dry stall, clean hay stored away from the horses, and a daily routine that keeps urine and dust from building up where your horse breathes.

Miles Henry

About Miles Henry

Racehorse Owner & Author | 30+ Years in Thoroughbred Racing

Miles Henry (legal name: William Bradley) is a professional horseman based in Folsom, Louisiana. He holds Louisiana Racing License #67012 and has spent over three decades managing Thoroughbreds at premier tracks including Fair Grounds, Delta Downs, and Evangeline Downs.
Expertise & Hands-On Experience: Beyond the track, Miles has decades of experience in specialized equine care, covering everything from hoof health and nutrition to training protocols for Quarter Horses, Friesians, and Paints. Every guide on Horse Racing Sense is rooted in this “boots-on-the-ground” perspective.
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