How to Muck Out a Stall for Your Horse’s Health


While we all wish that horses were tidy creatures that pick up after themselves, we must keep their living environments clean. This includes outdoor spaces, paddocks, runs, turnouts, whatever you want to call it, and their indoor stalls or sheds. And so we must muck out a stall or paddock in the best ways to keep our horses healthy.  

Table of Contents

Reasons to keep your horse’s stall fresh and sanitary

Types of horse bedding

Methods of bedding stalls 

The best ways to muck out a stall

When to strip your horse’s stall

Horse management tips for more sanitary stalls


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Reasons to keep your horse’s stall fresh and sanitary


  • Aside from the obvious reasons to keep your horse’s stall and bedding clean, there are health consequences if mucking is not up to par. 

Insects and rodents


  • Nothing says “welcome flies and rats” more than a dirty horse stall. Manure has a delicious aroma that lures insects, like biting flies. Dropped feeds and pellets entice rodents to visit for a snack.



  • Rodents love to live within about 20 ft of their favorite food source. Lots of leftover pellets and dropped grains give mice and rats a reason to nest in your barn. Yes, barn cats and dogs help, but it may not be enough. There’s also a risk of hantavirus when cleaning rodent droppings, so there’s that to consider. 


up close of a house fly

Flies LOVE stinky bedding



  • Another not-so-great situation in your horse’s stall is mold. This fungus will find a home when the conditions are damp, muck like wet shavings, or wet hay bits provide. Horses served wet hay or dunk their hay love leave gooey wet patches perfect for moldy science experiments.

Manure and urine stains


  • Perhaps the most annoying part of horse ownership is the appearance of stains and smelly patches on your horse. They are certainly easy to see on gray horses, but manure and urine stains land on all colors of horses. Aside from being visually unappealing, manure and urine patches attract flies, damage the hair, and create a dull finish on your horse.  


  • If you are tempted to blast manure and urine residue away, you will remove valuable sebum. Sebum is the main reason horses are shiny, *mostly* stain repellent, and waterproof. Keeping your horse in clean bedding helps alleviate all of this. 



Ammonia fumes


  • That blast of bitter ammonia smell can overwhelm anyone’s nose. Ammonia happens as urea in your horse’s urine breaks down. Unfortunately, it is also damaging to mucus membranes and your horse’s lungs. It’s worse if your horse eats from the ground; his nose gets even closer to those fumes. 


  • Ventilation in the barn is essential, even during winter. Destroying the odor is your next step. Ag lime, also known as barn lime, has been a staple in many barns for this very job. However – it can get slippery and only covers the odors up.  


  • On a side note, hydrated lime is a HUGE NO for horses or any other animal. This type of lime is caustic and will cause burns on the skin. 


  • Zeolites and baking soda are better options. Zeolites are tiny crystals that absorb the ammonia odor. They also absorb any residual wetness in stalls and can even freshen up stinky helmets and boots. Baking soda is also good but gets goopy. You’ll need to buy baking soda in bulk to beat the price of zeolites. 




  • The type of bedding that your horse rests on should be as dust-free as possible. The volume of dust in shavings directly impacts air quality and therefore impacts your horse’s lungs. 


  • Barn chores like sweeping and grooming can float the dust around, especially if you use a blower to sweep the aisle. Hay is another source of dust and may vary from load to load. 


  • Keeping dust to a minimum supports healthy respiratory function. 

Skin health – especially the lower legs


  • Lower leg skin infections can be challenging, expensive, and long-lasting. What we know as scratches, mud fever, and photosensitivity all fall under the umbrella of equine pastern dermatitis (EPD). Many factors lead to EPD on your horse’s legs – mites, bacteria, fungus, UV light, liver problems, and even tiny cuts or scrapes. 


  • Dirty shavings do not help this at all. Manure bits in the shavings are bacterial hot spots, but there is often a moisture component to some causes of EPD. Rinsing or bathing your horse and then popping them back onto shavings with wet legs may exacerbate brewing issues.


  • For horses with scratches or another type of EPD, keep a barrier between your horse’s skin and the outside world.  This includes shavings!  Your horse can wear specially made socks for horses, integrated with silver fibers.  Your vet is the best source of diagnostics and information to help your horse heal from skin issues.  



Yes, your horse can wear socks.  These are magical Silver Whinny’s. 


The type of horse bedding matters


  • Looking beyond budget and availability, bedding for your horse needs to check off a few boxes.  


  • It would be amazing to find low dust and high absorbency shavings. You can always combine shavings for a custom horse house. It seems logical that dustier bedding absorbs better, so put that as a base layer and add fluffy low-dust shavings on top. Using pine pellets as a base, topped with large kiln-dried shavings works well for some horses. The kiln-dried flakes keep the dust down.


  • Cedar-based bedding is excellent for outdoor areas. It’s a bit dusty but is fantastic in rainy conditions. 


  • Consider your storage options, too. Can you accept bulk deliveries? Some mills will deliver sawdust to barns, and the dustiness varies.  

** If you get shavings and sawdust from a lumber mill, they must never process black walnut. Even a tiny amount of black walnut in a horse’s stall triggers laminitis and swollen legs within hours. **

empty hay net over stall mat


Methods of bedding stalls


More is better (sometimes)


  • Deep bedding in stalls works best for tidy, non-tornado-like horses. Thick, fluffy beds also help prevent hock sores, pressure sores, and sometimes even shoe boils. The deeper bedding can be a pain to sift through, though. There is little rhyme or reason to making your horse’s stall like this; you add shavings until you need a map and compass to find your way out.

Go with the deep litter system


  • The deep litter bedding system modifies the typical deeply bedded stall. Here, the walls are banked, and the middle of the stall is flat. When mucking, remove the manure and the wet spots. Be diligent about not disturbing too much of the bed. Fill in any gaps by pulling down shavings from the banks.


  • A horse will pack down the bed, leaving a nice cushion that can last several weeks. Ideally, a tidy horse that urinates and poops in the same spots without dancing upon things makes the best candidate for deep litter. 




Less is more – you can skimp on shavings (sometimes)


  • Some barns use minimal shavings. Stalls with lovely mats or stall mattresses provide enough cushion, and shavings are mostly for urine only.  


  • Horses with in-and-out runs can also have another pile of shavings outside to encourage doing their stuff out of the stall area. It’s also helpful when your horse likes to sleep in the outdoor space, and many will do so when it’s safe and comfortable.

Banked walls 


  • With almost any type of shaving, any stall can have a banked wall. Letting the shavings pile up along the edges serves two purposes. One, you have a clean supply to refresh the stall close at hand. Two, banks can discourage horses from getting cast by prompting them to sleep in the middle. 


horse sleeping on banked shavings in stall

The best example of banked walls in the universe


The best ways to muck out a stall 


  • And now the most important part – actually mucking your horse’s stall or shed. 

Get the manure out


  • Hopefully this is easy, and there are no hidden piles or balls under the top layer of shavings. Many horses stir everything about, making stall cleaning a game of “Where’s Waldo – Poop Edition.”


  • For chaos poopers, you could sift through it all in a grid pattern or pile all of your sifted shavings into one corner. Or set up a poop net, tossing bedding against a grate tilted in a bucket. Shavings will fall through, and the stopped manure rolls into the bucket.  


  • If you use the deep litter bedding system, carefully extract the manure. It should be sitting on top of the bed. The deep litter system may work if your horse hides his manure.


  • For sparse shavings, use all of your saved time doing another chore. A bit of shavings on a stall mattress is so quick to clean!


yard tool broom cleaning

Wall clips are great for storing your stall cleaning tools


Dealing with urine


  • To remove urine spots, rake away any dry top layers. Using your manure fork, remove most of the wet shavings. For lovers of precision, use a snow shovel to scrape up any last bits of damp bedding.  


  • Sprinkle zeolites or baking soda on those spots to blast away any ammonia. Cover up the spot or let it air out for a while.

Don’t forget about these areas in your horse’s stall


  • Any place where your horse can drop something is a place to clean. Slobbery food bits, drool from waterers, and manure and urine down the walls need attention.  


  • Don’t overlook any snaps or latches that hold bins in place; these spots love to get caked with horse mystery goo. 


  • You can go the elbow grease way for dirty stall walls or give yourself a break and use a cleaning brush attachment to your power drill. BAM – clean walls, and fast. 


hand holding sweet pdz zeolite granules

Zeolites are also great for freshening up stale helmets and questionably smelling gloves.


When to strip your horse’s stall


  • It’s a gray area as to when to strip a stall. Usually, you will start to get that feeling when the shavings look dirtier and dirtier, you notice more flies, or there’s a different smell.  

It’s *mostly* easy to strip a stall, and you can skip the gym on that day. 


    • Remove all shavings, buckets, and tubs.
    • Scrub the walls as needed
    • Deal with the mats
    • Put it all back together

What’s under the mats?


  • When the mats are over dirt and clay, any urine getting through will warp the ground and mats under your horse’s weight. Rainwater can dampen the areas under your stalls and warp the floor and mats.


  • Some barns have drainage, gravel, or sloped stalls to facilitate drainage and prevent warping. 


  • Some stalls are concrete underneath, in which case you may need to straighten the mats. Mattresses exist without seams and don’t need much care unless there’s a tear. 


  • If you need to pull your horse’s mats, vice grips are a magnificent substitute for your hands. You can also fold your mats with a broom inside the fold and pick them up.  


  • Smooth out the base, perhaps let it dry out a bit, then pop the mats back with fresh bedding, and you are done! 

large gravel under stall mats for drainage

Gravel under mats can help with drainage


Horse management tips for more sanitary stalls


  • More turnout is the solution to many horsemanship, barn management, and horse health chores. It’s not always possible – so we all do the best we can.  


  • Pick your horse’s stall, shed, and paddock as often as possible. Learn your horse’s habits, and he will certainly make it easier for you. For example, most horses will poop not long after their first hay or feeding of the day. Wait a bit after that before you clean stalls.  


  • Combine shavings types for max urine absorption. It’s time to experiment with bedding, finding the best combo for your horse’s habits. 


  • Give your horse alternative options if there is an attached run or in-n-out. An “outdoor bathroom” if you will. Tossing semi-dirty shavings from the stall into a pile in the attached paddock gives your horse an absorbent place to urinate outside. Sunshine and wind quickly eliminate ammonia. Hopefully, this lures your horse into staying outside for his business.


  • Sweeping after watering the aisle reduces dust and allergens, helping to keep the barn and everyone’s lungs happy. Use a watering can to sprinkle water (or water and Pine-Sol mix) for best results.  


  • Soak or steam your hay to reduce the dust. Soaking and steaming provide similar benefits to some horses, and cut the dust for everyone. But, you may find those wet remnants of hay. 


snow shovel for loose bulk shavings

For more than just snow.


There is no perfect way to keep horses. They are unique individuals, and we all have different farms and barns. You can find the best ways to care for your horse and his environment in any circumstance, which means happier horses and people. 


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