How to Prep Your Barn and Horse for Fly Season

If you've ever spent a July afternoon in the barn swatting at flies while your horse stomps and tail-swishes in misery, you know fly season is no joke. Beyond the annoyance, flies spread disease, cause skin infections, and can make horses dangerous when they're head-shaking and kicking at their bellies.

The ultimate hack is starting your fly battle before you actually have bothersome flies. When it's still chilly, preparing for summer flies may feel premature. But trust us, once you're in the thick of it, you've already lost. Early spring is when you want to get your systems in place.

The Unglamorous Truth: It Starts With Poop

Flies breed in manure. Shocking, we know. But here's what most people don't realize—they also love wet bedding, moldy hay, spilled grain, and basically any damp organic mess you've been meaning to clean up. So your first job is to stop giving them free real estate.

Pick stalls daily. If you can swing it, pick twice a day during summer. And don't just chuck manure over the fence and call it done. That pile fifteen feet from your barn? That's a fly factory. Move your manure pile at least 100 feet away and learn to compost it properly. Hot composting—keeping the pile above 130°F—actually kills fly larvae. A cold, wet manure pile is just a nursery.

While you're at it, look at the spots you usually ignore. Under the feed bins. Behind the water trough. That corner of the wash stall that's always a little damp. Flies don't need much—a puddle under a leaky automatic waterer is enough. Fix leaks, improve drainage, clean gutters, and get rid of standing water before mosquitoes join the party.

Get Serious About Manure

Since we're already talking about poop, let's get into the details. If you've got space, set up a three-bin composting system. Fresh manure in bin one, decomposing stuff in bin two, finished compost in bin three. Turn it weekly to keep it hot. This kills fly larvae and gives you good fertilizer for your pastures.

No space or time for that? Pay someone to haul it. Commercial manure removal services usually come weekly, which is often enough to interrupt the fly lifecycle—flies take about 7-10 days to go from egg to adult, so weekly removal keeps you ahead of them.

Another option: spread manure thin on pastures you're not currently using. Sunlight and air dry it out fast, which kills larvae. Drag or harrow it to break up piles. This works, but don't spread on pastures about to be grazed—nobody wants their horse eating off manure-covered grass.

Make Your Barn Miserable for Flies

Once you've dealt with breeding sites, make the barn itself somewhere flies don't want to hang out. The single best investment? Fans. Lots of them.

Flies are terrible fliers. Get air moving around 5-8 mph, and they can't land. Put fans everywhere—in stalls, in the aisle, in the grooming area. Position them so they blow across each other, avoiding dead zones. Your horses will appreciate the breeze, too.

If you've got the budget, screen your windows and doors. At minimum, screen the feed room—nothing attracts flies like molasses in your grain. Automatic door closers are worth it, too, because someone will always forget to shut the door.

Those automatic fly spray systems that mist the barn on a timer? They work well in enclosed spaces. If you've got an open-sided barn, you're just spraying into the wind. 

Fly strips and traps have a place, but don't hang them right where near grooming or working areas. The strips contain attractants. The whole point is to lure flies away from the barn, not create a buffet line next to the cross ties. Change them regularly. A trap coated in dead flies stops working and is just plain disgusting.

Don't Forget the Pastures

Flies don't care about property lines. Your pastures need attention, too.

Rotate grazing to avoid bare, muddy paddocks. Mud + manure = fly heaven. Drag pastures regularly to break up manure piles and expose larvae to the sun and predators. Speaking of predators, birds eat tons of flies. Put up some bluebird boxes or let barn swallows nest in your eaves—they're messy, but they earn their keep.

Fix drainage problems. Fill low spots, improve boggy areas, or fence them off entirely. If you have a pond, stock it with fish that eat mosquito larvae. Goldfish and koi work great, and they're pretty to look at.

Stock Up on the Gear

Buy your fly stuff early, before everyone else realizes it's fly season. You'll need fly spray, fly masks, fly sheets, and leg protection if your horse stomps hard enough to hurt himself.

Fly spray options are overwhelming. Natural pyrethrin breaks down in sunlight but won't irritate sensitive skin. Synthetic pyrethroids stick around longer. Permethrin works on both horses and their environment. Read labels, try a few, and rotate products so flies don't get used to any one thing.

Some horses need full body armor. Get them a good fly mask—some styles cover ears, add nose pieces, and even block UV. Fly sheets keep bodies protected without overheating horses in summer. For horses that stomp constantly, fly boots prevent injuries. 

Pay Attention and Adjust

Watch what's working on your property. Perhaps fans alone make a huge difference. You may need the full arsenal. Figure out which areas get hit hardest and focus there. Watch your horses for excessive tail swishing, head shaking, stomping, skin sores, or goopy eyes mean flies are winning. 

The Reality Check

If you start early, layer your defenses, and stay consistent, you can keep fly populations low enough that your horses aren't miserable and you're not spending your entire summer swatting.

The work is worth it. Clean up early. Use fans. Manage manure properly. Protect your horses. Stay on top of it—skip stall cleaning, and you'll undo your progress.

Your horses will be more comfortable, which means they will be happier to handle and ride. And you'll spend a lot less time standing in the barn aisle with a fly swatter, which is time better spent actually riding.

References

1. Zinni, Y. (2022). Life cycle of a horse fly. Sciencing. https://www.sciencing.com/life-cycle-of-a-horse-fly-12531030/

2. Pest Help. (2024). House fly life cycle & reproduction. https://www.pest-help.com/pests/flies/house-flies/house-fly-life-cycle/

4. Terminix. (2025). Fly life cycle: How long do flies live? https://www.terminix.com/other/flies/life-cycle/

5. Perennia. (2018). The biology and lifecycle of common flies in livestock operations. https://www.perennia.ca/wp-content/uploads/2018/04/the-biology-and-lifecycle-of-common-flies-in-livestock-operations.pdf

6. Oregon State University Newsroom. (2024). Don't worry, maggots help break down compost pile.https://news.oregonstate.edu/news/don%E2%80%99t-worry-maggots-help-break-down-compost-pile

7. Aptive Pest Control. (2025). How fast can a housefly fly? https://aptivepestcontrol.com/pests/flies/house-flies/how-fast-can-a-housefly-fly/

8. Biology Insights. (2025). How fast can a fly fly? Their top speed in MPH. https://biologyinsights.com/how-fast-can-a-fly-fly-their-top-speed-in-mph/

9. Insect-O-Cutor. Interesting information about the housefly. https://www.insect-o-cutor.com/flyfacts.shtml

10. Horse and Rider. (2023). Fly control options for horse and barn. https://horseandrider.com/how-to/fly-control-horse-barn/

11. Penn State Extension. Horse stable ventilation. https://extension.psu.edu/horse-stable-ventilation

12. Purdue University Extension. Horse and deer flies. https://extension.entm.purdue.edu/publichealth/insects/tabanid.html