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Chickens,  Our Homestead

Homestead Update: Deep-Cleaning the Chicken Coop

Well friends, we officially tackled our first big project at the new homestead: preparing and deep cleaning the chicken coop that we inherited. Excuse my French, but talk about a sh*t show! Literally. (You’ll see what I mean soon) Don’t get me wrong: I’m incredibly grateful to not have to start completely from scratch! But oy vey, this place needed a LOT of elbow grease to get to a level that I felt comfortable moving our girls into. After all, we can’t move in until the girls can move along with us!

So, come along and look at plenty of pictures of poo while I walk you through the process we took to clean, sanitize, rehab, and refresh the existing coop and run while also addressing concerns about biosecurity, predators, parasites, and more.

I should mention that I don’t want this scene to overwhelm or deter anyone who may be on the fence about getting chickens! The condition of this coop was NOT normal, and easily avoidable with more routine (and less cumbersome) cleaning. I find it even easier to keep a smaller coop clean, like our old coop. If you’re considering or new to chicken keeping, stop by our “Backyard Chickens 1010: What to Expect When You’re Expecting” article.

Before. It’s hard to tell, but the litter and poop is nearly a foot deep along the back wall there!
After. So fresh ‘n so clean!

The State of the Coop-ion

The existing chicken coop is a converted 8×12’ shed with an attached 18×18’ fenced run. It sits about 30 feet to the right of our back patio, and I love that we can easily keep an eye on them from there – as well as from our upstairs bedroom balcony. From what I can gather, the coop was installed in either 2016 or 2017. 

No offense to the previous owner’s… but it seems like perhaps they were attempting to use the “deep litter method” (but not correctly) or the coop was simply neglected, because we were left with what appeared to be about 5 years worth of chicken poop to deal with. It’s hard to tell from the photos below, but the bedding on the floor was about a foot deep in some places. There were two extra-large cat litter pans poised below the old roost that were completely overflowing with crap. 

And let’s not forget the window… The nesting boxes were positioned in front of a window and secured in place. If you know chickens, you know they like to perch (ahem, sit and poop) as high as possible, which is why I always suggest keeping the nesting boxes lower than any other available roosts. The top of these old nesting boxes was the highest perch point in the coop. So naturally, they hung out there – and pooped into a void between the backside of the nest boxes and the window behind it. The result = years of accumulated poop in the open screened window.

Alright, I think you get the picture… but just in case, here are some photos:

Extra large cat litter pans overflowing with poo.
The infamous poop window. The whole sill and track was full, inches deep in every direction.

Biosecurity & Pest Concerns 

Trust me friends, I understand that chicken coops aren’t going to be pristine! And it’s one thing to have your own chickens living in certain conditions. Yet there was no way in hell I was going to move our girls into this place without a thorough and deep cleaning – for everyone’s health and safety. In addition to being downright gross, we had no idea about the health of the previous flock and potential issues that could be lurking in the contents of the old bedding, poop, and coop or run.

Things I was concerned about and needed to assess or address:

  • Adequate predator-proofing
  • Potential disease, bacteria, pests and parasites 
  • General cleanliness (e.g. dust control, odor, leaf litter accumulation on the run, etc)
  • Functionality – both for us and the chickens 

Let’s talk about the first two now, then I’ll get more into functionality later as I share the changes we made to the inside. 

Chicken Coop Predator-Proofing

Chickens have more predators than most folks imagine! On this particular property, the primary chicken predators we’ll have to contend with include hawks, owls, coyotes, raccoons, skunks, and opossums. Someone mentioned we may also have weasels in our area, which also kill chickens. In other places, fox, bears, bobcats, or mountain lions and other large predators or birds of prey could be of concern. You also don’t want rodents or snakes to get in, as they’ll threaten the eggs, feed, and generally become a nuisance.  

The very first thing I did with the new chicken coop was a perimeter check. I was pleased to see that they used hardware cloth for the run, as a skirt under the coop, and over the windows. Hardware cloth is the best option for predator-proofing a chicken coop area since it’s incredibly durable and has very small openings for any critters to slip through. 

Despite the misleading name, “chicken wire” shouldn’t be used for predator-proofing a chicken coop or run. The holes are large enough for mice or some rats to squeeze through, and it’s not very strong at all. Certain animals can tear through it, rodents can chew through it, and it also degrades, rusts, and weakens significantly with time.

Side view of the new coop and run.

However, as I cleared off branches and leaf debris from the top of the run, I did find a number of large gaps in the hardware cloth over the top (big enough for an opossum or raccoon to enter) as well as some rodent-size gaps along the sides. We don’t have the time to fully batten down the hatches before the girls move over, but I was able to close up the biggest gaps with large zip ties for now. 

At this point, I consider the run safe for daytime use, but we’ll close up the coop overnight just in case anything sneaks in then. The coop itself is pretty sound. We’ll eventually add an automatic chicken door that will open the coop to the run at dawn and close again at dusk.

As I removed branches and leaf debris from the top of the run, I found several large and small gaps in the hardware cloth. The one to the left is large enough to let in opossum, raccoons, and more.
I was able to close up the largest gaps using several heavy-duty zip ties (for now, I’ll add more wire later) but there are many rodent-size gaps still open around the run we still need to address.

Disease and parasites

After the predator safety check, it was time to tackle deep cleaning and sanitizing the inside of the chicken coop. You’ll see our step-by-step process below, which included carefully removing all the contents of the coop, washing and sanitizing the inside, installing a new easily-cleanable floor, new nest boxes, roost, and applying lime in both the coop and run. 

My main concerns were potential for lurking poultry lice, mites and general bacteria and dust, followed by Marek’s disease and any other disease that inflicts chickens. The virus that causes Marek’s disease can reportedly live for up to 5 months in the environment, and the last flock moved out of this space about 4 to 5 months ago, so we’re right on that threshold. Our girls were vaccinated for Marek’s as chicks, though that isn’t always 100% effective. Because the soil is super dry here 99% of the year, parasitic worms aren’t a huge concern but also something I had in mind. 

For us humans, I was worried about histoplasmosis – a harmful fungus that lives in bird and bat droppings, and can result in serious illness if inhaled. Therefore, OF COURSE we thoroughly masked up, and worked slowly and methodically in an effort to not stir up any more dust and movement than necessary while we worked. 

Deep Cleaning the Chicken Coop

Step One: Removal

The first couple of days of deep-cleaning the chicken coop was spent clearing out everything from inside: the deep poopy bedding, poop-filled cat litter trays, old nesting boxes, and old roost. We ended up filling ten 40-gallon trash bags full of bedding and poop! And poop is much heavier than one may imagine… No, we didn’t fuss with composting any of it because a) all the biosecurity concerns I just mentioned above b) we don’t have a proper compost system set up at the new homestead yet, and c) we simply didn’t have time to mess around. We needed this thing chicken-ready, pronto. 

Again, we took great care during this process to move slowly, wear masks, and stir up as little dust as possible. Rather than dumping shovel-fulls inside the coop itself (and creating dust clouds) we kept the trash can outside the coop door where it could air out. While Aaron worked on clearing out the inside (bless his soul!), I was busy removing branches and leaves from the top of the run – using a combination of a push broom from above and my new favorite battery-powered leaf blower from below.

We used a wide flat shovel to remove the accumulated poop and bedding.
Using a combination of a push broom from above and a leaf blower from below, I was able to clear most of the debris from the top of the run.

Day two of removal was just a quick one after work, but an especially gross (and honestly, comical) task: removing the old nest boxes that had caused the infamous “poop window”. As we pried the very attached nest boxes away from the wall, a literal cascade of sh*t came pouring down from behind it as we ran from the coop. Even then, a several inch thick wall of poo was still stuck in the window, so next we poised a trash can below it, and Aaron pushed on the screen from the outside to get the poo wall to fall forward and into the can – while I filmed and laughed. Then I got in there and finished the job from the inside. 

This was simply poor design… Knowing chickens, of course they perched on top of those nesting boxes – and pooped into the window behind it.

Step Two: Cleaning & Sanitizing

Next, it was time to hose this baby off. Some folks suggested a pressure washer, but that strong  of a blast in a confined space would have just sent poopy water splattered everywhere – including on me. So instead I started with a gentle “shower” spray to knock all the dust down first. Then I switched to a firm jet stream and went over all the walls and floors again. The water pooled in one area of the coop so we used an old push broom to usher it out the door. 

Once all the standing water was out, I sprayed everything down with several coats of plain undiluted white vinegar by adding it to a garden pump sprayer, and focused on the heavily soiled areas the most. Vinegar is an excellent natural sanitizing agent, albeit not quite as strong as bleach (I wasn’t keen on coating the space with bleach, especially because I was going to be in there working, and even spraying the ceilings above me).  

Because the chicken coop is a plywood-based shed, it was important for it to dry out as quickly as possible thereafter in order to not warp or ruin the plywood. We had brought over a box fan from the old house and set it up in there with the coop door and all 3 windows open. It was totally dry 24 hours later. I also needed everything to be dry before we proceeded to the next step, adding a new floor.

Before and during getting sprayed down with water.
Aaron removing the soiled water (that of course pooled on the opposite side of the door). Yes, a big squeegee would have been more effective, but we had very few tools or supplies at the new house with us yet!
Now time to spray/sanitize everything with white vinegar. I used a full gallon.

Step Three: Install New Flooring

Next, we added sheet vinyl (laminate) to the bottom of the chicken coop to create an easily-cleanable and nonporous floor. That’s what we have in our old smaller coop, and it makes routine deep-cleaning of the chicken coop much easier! The coop shed is 8×12’ and we found that our local Home Depot carried sheet vinyl in that exact size, though you could also order a larger roll and cut it down as needed. 

First, we unrolled the vinyl out on our patio in the sun for a few hours to get it to relax and lay flat. Then we brought it inside the coop and quickly realized it was a bit too large, so we aligned it along two sides of the walls and used a razor blade (box cutter) to cut off the excess from the others. Next I pulled up/back half of the vinyl and applied a strong construction adhesive (rated to bind to wood, plastic, and vinyl) all along the sides and middle of the existing plywood floor below, laid the vinyl back down over it, and walked all over it to squish it all down. Then we repeated the process on the other half. 

Finally, I added a handful of roofing nails along the perimeter to provide extra hold – in the corners, along the doorway, and in a few odd raised spots. That step probably wasn’t totally needed because the adhesive bonded quite well, but I had the nails already so… just in case! 

All dry the next day, fitting the sheet vinyl floor (which needed to be cut down to size)
Applying construction adhesive to secure the new floor down. Looking (and smelling) a world better already!

Step Four: Dust for Pests & Parasites

Though the walls had been sprayed down and sanitized, I still hadn’t done anything to address potential mites, lice, or similar pests at this point. Poultry lice and mites are tiny parasites that feed on chicken skin, blood, and feather parts… Gross, I know. Even more, red poultry mites are known for hiding out in between wood boards, roosts, nesting boxes, and similar crevices – and can live for many weeks without a meal! So the next step was to dust the walls, beams, corners, and perimeter of the new floor with lime powder. (We didn’t dust the old floor first so that the adhesive would stick). 

I dusted everything using First Saturday Lime, including the dirt in their run. It’s a natural, nontoxic, and pet-safe pest product that desiccates (dries out and kills) any insect with an exoskeleton – inducing mites, fleas, lice, ants, beetles, and ticks. It has a very similar method of action to DE (diatomaceous earth) but doesn’t pose the same respiratory risk as DE, a natural silica-based substance. Food grade-DE is technically non-toxic to humans and mammals, is safe to consume, but shouldn’t be routinely inhaled. I know many chicken keepers use DE; we did for years as well. We’ve been transitioning over to lime instead.

Dusting the floors, edges, walls, and supports with lime. Food-grade DE and lime are two options for controlling pest insects and parasites in a chicken coop, though we’ve been using lime over DE lately.
Lime in the run as well. I also have to give a big shoutout to our favorite waterproof garden and chore boots – Merry People! We each have a pair, and are even more glad to have them on this type of property. They’re incredibly comfortable, supportive, and protected our feet during this dirty job! Check out Merry People here (affiliate link)

Step 5: Fresh New Additions

Now, let’s make this house a home! Using random scrap wood we already had around the homestead, we whipped up a new set of nesting boxes and a basic roost. Fresh pine shavings went on the floor as bedding, and I also sprinkled a little lime around in that too. We also brought over their favorite sawhorse roost for the run.

As a roost, I like to give the gals a flat board (a 2×4” on it’s wide side) instead of a round dowel or branch, and they seem to prefer it too! After all, I can only imagine how much more comfortable and stable it is to settle in for the night when you don’t have to wrap your feet tightly around something to hang on. I intentionally used more narrow 2×2” side supports to encourage them to sleep on the main wider roost instead, since that is positioned over the poop board. 

Poop board, huh? Just like in our old coop, we created a poop board that sits below their roost. It’s simply a piece of plywood wrapped in sheet vinyl that is glued in place. The idea is that 90% of their coop poop ends up on that board, and then we can easily scoop it up every day (or every other day) using a wide paint scraper and dust pan. It keeps the coop so much more clean, tidy, and odor-free! The vinyl makes it easy to periodically wipe down and sanitize too. 

New roost and poop board with fresh pine shavings down on the floor.
We also created a temporary door for the coop since the run isn’t fully buttoned up yet. We’ll eventually put in an automatic door.

In regards to the nesting boxes, we really only needed two for our four hens, since chickens prefer communal nests and often lay in the same box anyways – but figured, hey why not add another? We kept that on the coop floor since that is what they were used to in their old coop, and also to discourage sleeping in the nesting boxes. 

99% of the time, chickens will roost (and poop) at the highest point of the coop at night, so it’s always best to keep nesting boxes at a lower elevation than their roosts. The previous nest boxes were the perfect case-in-point: that’s what caused the infamous poop window! The top of the nesting boxes was the tallest thing in the chicken coop. I’ll write a separate how-to for building the next boxes soon, for those interested.

Basic nesting boxes. We love using these nesting box pads to line each box. They help prevent cracked eggs, and provide a comfy spot for the girls to curl up in.
Checking out the new digs!

Step 6: Moving Day!

Or should I say, moving night? Did you know that chickens can’t see in the dark? That is why they instinctively find an elevated roost come dusk. That said, chickens are typically far easier to handle and seemingly more calm (maybe just scared and still?) in the dark or night. So that makes it a great time to quietly slip them into a new environment, add a new chicken to a coop, or even swap eggs for baby chicks under a broody hen. 

The first evening we were ready to stay in our new place, we headed back to the old house to collect the girls after the sun went down. We loaded them up in a combination of cat crates and cardboard boxes (with air holes) and puppy pads on the bottom. Still working in the dark, I plopped each one down on their new roost and said goodnight. Come morning, they were mildly cautious to get down and explore their new digs – but with a little coaxing and black oil sunflower seeds, they were happily scratching around in no time!

Early the first morning after the move. They weren’t sure about getting down at first, but warmed up to their new environment quickly thereafter!
Weee! Thanks Mom!

Going Forward

So we finished deep cleaning the chicken coop… now what? Many of you have inquired if bigger coop = more chickens for us? For now, nope! We don’t plan to add to our flock any time soon. Four chickens provide us with more than enough eggs, egg-citement, and clean-up! Also, because we have more predators at this property and they’ll therefore be spending most of their time in the run, I love that they have ample space per bird rather than crowding it. The minimum recommended run space for chickens is about 10 square feet per bird, and 3 to 4 square feet in the coop per bird.

The next thing we’ll be tackling is adding a couple vertical supports to the sagging run roof using 4×4” boards and concrete footers. Those supports will double as a place to attach branches to create a daytime “tree” to roost in. I also want to make a nice landscaped pathway from our patio to the coop – you know, so I don’t twist my ankle in gopher holes, and have a dry and clean path on our few rainy days here. Finally we need to continue to patch up the small gaps in the hardware cloth around the run, and maybe add a few solar spotlights to further deter nocturnal predators.

From grimy to glamorous!

And that’s the story of how we transformed our inherited “poop coop” to a pretty, clean, functional, and safe environment for our beloved flock. I hope you enjoyed reading along with this messy task, and picked up a few tips on deep cleaning a chicken coop if needed! If you happened to miss the story of our move to this new homestead, read more about it here, and then be sure to check out the related chicken articles below! Thanks so much for tuning in.


  • Colin

    Thanks for the detailed posting! We’re getting into chickens here in suburbia, which is not easy to do in our county, unfortunately. I’m gathering ideas for a coop and this is really helpful info. We raised 4 abandoned chicks for a month in a large dog cage and really enjoyed them, but 3 of them turned out to be roosters, which are banned in our county on less than 7 acres, so we’re starting over!

  • Jamie

    Wow! What a big undertaking! Your four hens have so much more space than my four. We just recently did a coop cleanout and used DE (we love DE) as our pest repellent. I really like it, but I am curious about trying Lime in the coop. Thanks for the info!


  • BlackBetty

    I see your new coop has a run, what do you put in the run section outside to keep it from getting slippery and gross? Struggling to find something that works well for the run for my ladies that I can easily remove when it gets full of crap. Gravel is good for drainage but doesn’t allow me to “clean up” the poop.

    • Aaron (Mr. DeannaCat)

      Hi Betty, you can use sand or washed concrete sand which still allows for drainage and doesn’t get too messy when it’s wet out, it also stays fairly firm so the droppings will remain on the surface. Good luck!

      • Theresa

        I don’t have a coop just a big chicken run. My husband made nest boxes for them but the chickens sleep up top on their boxes he made. He made the nesting boxes for them on the other side. The floor is dirt and it’s hard work to get it cleaned. He doesn’t help with the chickens.

        • Aaron (Mr. DeannaCat)

          Chickens like to roost up high, if the nest boxes are taller than a roost they may sleep on, they will likely roost on top of the boxes. Maybe a roof that has an angle to it will stop the chickens from roosting on their nest boxes, if they don’t have a roost, I would make one with a 2×4 for them. Good luck!

  • Susie

    I had a variety of chickens for several years and found these things helpful:

    – remove any ‘manufactured wood’ (2×4: 2×2, large dowels etc) and bring in some similar size tree limbs or big sticks – the birds love them!

    – buy an exterminator’s very inexpensive ‘bulb duster’ and put powdered DE (diatomaceous earth) in it,…the one I bought came with 3 or 4 different ‘nozzles’ which let you spray in tight corners etc. DO NOT dust in an enclosed space without protection and ventilation!! DE will dry your eyes and nose/lungs! A large clear or frosty trash bag usually holds ample air and doesn’t have to be sealed tight around you…it doesnt usually take long but you can also take a break…at the end, i used the duster to ‘fog’ the coop inside, then exited promptly; the bag can be shaken out and reused. DE can be bought inexpensively by the pound and the highest (food) grade isn’t needed…a little goes a LONG way – any excess keeps well in a sealed container (I like wide mouth glass canning jar(s) as you can write contents on lid as well as glass face).

    – you can make a decent cheap hoop house from 4′ x 16′ panel(s) of ‘goat fence’…if the goats can’t chew through it, birds are pretty safe….sealing hoop house to coop can be tricky…hungry varmints can get sneaky. My coop was on wheels which was nice as I could move birds to new forage; there’s far too many foxes, hawks, and other predators here to let them totally free range except if I was out with them.

    My birds would come when called…trained them with tasty treat(s) — they learned fast! I would let them totally free and call them – they’d come running as they knew grains or apple peels or fruits awaited! Hope thats helpful….

  • Mims

    Wow, this is super impressive. I am in awe at your dedication to hygiene for chickens. You guys are the Florence Nightingale for poultry. Enjoy you new home, look forward to seeing how you make it yours.

  • Andrew

    Wow. Amazing work!

    Can I ask, are you keeping all that chook poop for compost / soil enrichment and if so what’s the plan there? Thanks! 😁

    • Aaron (Mr. DeannaCat)

      Hi Andrew, we didn’t choose to keep any of the poop or bedding for compost because we were unsure of how the chickens were raised and what may or may not be in their refuse. We were also trying to move into our current place while moving out of and taking care of our old place on top of cleaning up this coop so our hens would have a clean place to stay, there was too much going on in general to try and find a suitable place for hundreds of pounds of bedding and excrement on our new property to use at a later date for compost. Hope that helps and thanks for reading.

  • C.E.

    Wonderful post/story!
    As a wannabe chicken mamma, how do you address the watering/feeding side of things?
    Thank you for everything.
    Such a huge and marvelous new adventure for the two of you!

    • Aaron (Mr. DeannaCat)

      Hi C.E., thank you so much! We keep the hens waterer (2 gallon stainless steel) and feed (maybe 10 pound feeder) in their run, we change out the water on a weekly basis and refill their feed as needed. Hope that helps and thanks for reading.

  • TByrd

    I’m very happy for you both for finding such a wonderful new homestead!!
    My mother was an avid gardener and in my youth we grew almost everything we ate. Her 2.5 acres spot of earth was always full of lots of food and flowers, wild birds, and other animals that stopped by to feed. We all ate better because of her knowledge and our collective hard work.
    You’re going to love living there and making the property truly yours. And thanks for taking your readers along for the journey.

    • Aaron (Mr. DeannaCat)

      Hi TByrd, thank you so much for the kind words and hopefully one day we will resemble something close to your mother’s property.

  • Sheereen Hitner


    Thanks for posting this and all things chicken!
    I love what you’ve done with the place. 🙂 Lots of good ideas here that I am incorporating into my chicken coop.
    One question…how high up off the floor is the roost?

    Thank you and keep posting!

    • Aaron (Mr. DeannaCat)

      Hi Sheereen, glad you found some useful information to implement in your own coop. Our current roost that we just made for our hens is just shy of 18 inches. There are two 16 inch 2×6’s as the legs with a 2×4 sitting across the two legs as the main roost. Hope that helps and thanks for reading.

      • Michelle

        Hi Deanna and Aaron!
        I’ve been following y’all for years, congrats on the new place! My question is coop related, I recently added to mine and had to purchase hardwire. The roll came with a California prop warning (which is not common in texas). So I googled and went down the rabbit hole. Found the problem and no real solution. My potentially toxic galvanized metal fence (which is already up) is making me lose sleep and I’m willing to take down and purchase better. So my question to you guys is have you all encountered this problem with products? Do you know of a good stainless steel fencing option? Or any other solution for a secure coop run? hope y’all can help, I’ve found not much elsewhere:(

        Thank you both for sharing your homesteading knowledge!


        • Aaron (Mr. DeannaCat)

          Hello Michelle, thank you so much for the kind words, we really appreciate your support and for following along through the years! In regards to your coop/run, I don’t think you have anything to worry about. I am not sure the brand of hardware cloth you got but we use the Everbilt band of hardware cloth that you can find at Home Depot. In California, we see the Prop 65 warnings on a lot of things, I have even seen it at the entrance of apartment buildings. There may be a thing or two in galvanized steel that warrants the warning but we even use the cloth under our garden beds to keep gophers from wreaking havoc in our veggie garden. In all, you and your chickens should be just fine with your initial choice and I am sure they thank you for keeping them safe. Hope that helps and reach out if you have any other questions or concerns.

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