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How to Reduce Odour in Chicken Coops, Stables, and Feedlots Naturally

For small-scale backyard keepers and commercial livestock operators alike, odour management is one of the most persistent challenges in animal husbandry, and one of the most solvable.

Why Livestock Odour Is More Than Just a Nuisance

The smell coming from a chicken coop, horse stable, or cattle feedlot isn’t simply unpleasant, it’s a sign of active chemical processes that can harm your animals, your health, and your land.

The two primary culprits are ammonia (NH₃) and hydrogen sulfide (H₂S). Ammonia is released when manure decomposes and feed nitrogen isn’t fully converted into animal product. Hydrogen sulfide – the infamous ‘rotten egg’ smell – forms under anaerobic (oxygen-deprived) conditions as manure breaks down. 

Research published in Juniper Publishers (2019) confirms that both gases can cause chronic or acute pulmonary disorders in farm workers, and in animals like poultry and swine, ammonia concentrations above 25 ppm can damage respiratory tracts and mucous membranes, triggering disease and reducing productivity.

For neighbours and nearby communities, even low concentrations are detectable and can become a source of serious complaint or regulatory action.

The good news is, you don’t need harsh chemicals to fix it. Nature already has the answer.

What Actually Causes the Smell?

Before you can treat the problem, it helps to understand what’s driving it.

When manure accumulates in a confined space – a coop, a stable, a feedlot pen, putrefactive (rotting) bacteria dominate. These anaerobic microorganisms break down organic matter and release volatile compounds including:

  • Ammonia – from nitrogen in urine and faeces
  • Hydrogen sulfide –  from anaerobic decomposition of sulphur compounds
  • Volatile fatty acids (VFAs) – butyric acid, isovaleric acid, and others that contribute to the characteristic ‘farm smell’
  • Volatile organic compounds (VOCs) – including phenolics and dimethyl sulfide

The key insight is that odour is a microbial problem. It’s not the manure itself that smells, but the bacteria decomposing it. Change the microbial environment, and you change the smell.

Natural Methods to Reduce Livestock Odour

1. Effective Microorganisms (EM) - The Most Powerful Natural Solution

Effective Microorganisms (EM) technology, originally developed by Japanese agronomist Professor Teruo Higa in the 1980s, is now one of the most well-researched biological approaches to odour management in livestock operations worldwide.

EM products contain a stable consortium of beneficial microorganisms – primarily lactic acid bacteria, photosynthetic bacteria (such as Rhodopseudomonas spp.), and yeasts, that actively compete with and suppress the putrefactive bacteria responsible for foul odours.

How EM works:

Rather than masking smells, EM microorganisms fundamentally shift the microbial balance in the animal’s environment. By promoting fermentation over putrefaction, they:

  • Convert ammonia into stable, plant-available nitrogen compounds
  • Suppress anaerobic bacteria that produce hydrogen sulfide
  • Reduce the volatile fatty acids responsible for sour, rancid odours
  • Break down organic matter in a way that produces little to no offensive gas

What the research shows:

A 2024 study published in Fermentation (Park et al., Gunwi Agricultural Technology Center, Korea) fed a consortium of four microbial strains – Bacillus subtilis, Lactobacillus acidophilus, Lactobacillus casei, and Saccharomyces cerevisiae, to beef cattle over three months. 

The results were striking: ammonia in manure decreased by 64.1%, dimethyl sulfide by 81.3%, butyric acid by 84.6%, and isovaleric acid by 49.8% compared to the control group.

Research commissioned by the University of Applied Life Sciences in Vienna found that applying EM technology to solid manure reduced ammonia emissions by 45% with measurable improvements in stable climate and a significant reduction in fly populations. Veterinarian Dr. Joachim Kreuzinger, who has used EM technology in his practice since the late 1990s, states ‘since he’d been using EM his slurry was much more liquid and the fly population had radically depleted.

A study published in PMC (National Center for Biotechnology Information) on deodorising strains found that Bacillus subtilis alone achieved hydrogen sulfide reduction rates of up to 90.8% when applied by spraying.

2. Litter and Bedding Management

Even with EM, physical management of litter remains important. Moisture is the enemy as wet litter accelerates putrefaction and ammonia production rapidly.

  • Replace or turn litter regularly. In chicken coops, the deep litter method – where bedding is turned frequently and new material is added, can work well in combination with EM, as the microbial activity in the litter itself helps break down waste.
  • Use absorbent bedding materials such as pine shavings, straw, or hemp, which reduce moisture retention.
  • Remove caked or soiled patches promptly, particularly in high-traffic areas around waterers and feeders.

3. Ventilation

Good airflow is essential. Stagnant, humid air allows ammonia and hydrogen sulfide to concentrate. Ensure your structures have:

  • Adequate ridge vents, windows, or mechanical ventilation
  • Cross-ventilation that moves air through the animal zone
  • Airflow that doesn’t create cold draughts directly on animals in winter

Ventilation alone won’t solve a severe odour problem, but it’s an important part of the system — particularly for enclosed poultry sheds where ammonia can reach dangerous concentrations rapidly.

4. Dietary Adjustments

What animals eat directly affects what their manure smells like. Excess dietary protein that isn’t absorbed gets excreted as nitrogen – the raw material for ammonia.

  • Precision feeding – matching protein levels to the animal’s actual requirements reduces nitrogen excretion significantly.
  • Research from ScienceDirect (2023) identifies low-crude-protein diets with targeted amino acid supplementation as one of the most effective and underused tools for reducing ammonia emissions at the source.
  • Adding EM or probiotic cultures to feed shifts the gut microbiome, improving nutrient absorption and reducing odour-causing compounds in manure at the point of production.

6. Composting Manure Properly

Manure that sits in an anaerobic pile is a major odour source. Properly managed compost, turned regularly and kept aerobic, produces little offensive smell and creates a valuable soil amendment. EM can be incorporated into compost heaps to accelerate breakdown, suppress pathogens, and further reduce odour during the composting process.

Chemical vs. Natural EM Approaches in Livestock Odour

The Bottom Line

Livestock odour is not inevitable. It’s the predictable result of putrefactive biology taking hold in a confined environment. The most effective, sustainable, and animal-safe way to address it is to change the biology: replace the bacteria that cause rot and release toxic gases with microorganisms that ferment, stabilise, and enrich.

Effective Microorganisms (EM) technology does exactly that. Backed by decades of agronomic research and a growing body of peer-reviewed science, EM solutions offer livestock owners, from backyard chicken keepers to commercial feedlot operators, a proven, chemical-free path to a cleaner, healthier, and more pleasant operation.

The science is clear. The results are measurable. And for your animals, your workers, and your neighbours, the difference is immediately noticeable.

References

  • Park, M-K. et al. (2024). Probiotic Feed Additives Mitigate Odor Emission in Cattle Farms through Microbial Community Changes. Fermentation, 10(9), 473. https://doi.org/10.3390/fermentation10090473
  • Multikraft / University of Applied Life Sciences Vienna. Effective Microorganism (EM) in Animal Feed & Husbandry. https://www.multikraft.com/en/products-applications/animal-husbandry/
  • NCB/PMC. The Odor Release Regularity of Livestock and Poultry Manure and the Screening of Deodorizing Strains. https://pmc.ncbi.nlm.nih.gov/articles/PMC8705919/
  • Xu, S. et al. (2017). Odour reducing microbial-mineral additive for poultry manure treatment. Frontiers of Environmental Science & Engineering / Springer Nature. https://link.springer.com/article/10.1007/s11783-017-0928-4
  • Ning, X. et al. (2023). Control of odor emissions from livestock farms: A review. Environmental Research. ScienceDirect. https://doi.org/10.1016/j.envres.2023.115651
  • MSU Extension. (2015). The impact of ammonia and hydrogen sulfide emissions from animal agriculture. Michigan State University. https://www.canr.msu.edu/news/the_impact_of_ammonia_and_hydrogen_sulfide_emissions_from_animal_agricultur
  • Seo, J. et al. (2019). Regulation of odor gas emission and performance by probiotic Bacillus in livestock industry. Juniper Publishers. https://juniperpublishers.com/aaps/AAPS.MS.ID.555560.php
  • Cho, S. et al. (2020). Evaluation of Short-Term Exposure Levels on Ammonia and Hydrogen Sulfide During Manure-Handling Processes at Livestock Farms. PMC. https://pmc.ncbi.nlm.nih.gov/articles/PMC7078563/
  • Tyndall, J. & Colletti, J. (2000). Cited in: Ethnobotanical Control of Odor in Urban Poultry Production: A Review. Livestock and Poultry Environmental Learning Community. https://lpelc.org/ethnobotanical-control-of-odor-in-urban-poultry-production-a-review/
  • Desai, S.S. & Sangam, V.S. (2022). Manure biostabilization by effective microorganisms as a way to improve its agronomic value. ResearchGate. https://www.researchgate.net/publication/358507561

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