How to Clean for Coccidia [and get results]

To reduce the degree of coccidial infection in bearded dragons, cleaning to be a priority. Throughout the treatment period a thorough cleaning routine will need to be in place for at least 6 weeks. The quickest results will come by adhering to a daily rigorous and thorough daily routine to clean for coccidia.

The purpose of cleaning is to kill the oocysts that are in the bearded dragon’s environment waiting to be ingested. The less oocysts that are in the environment, the less the load your bearded dragon’s immune system will have to deal with. A single oocyst can turn into thousands quickly so there is no room to get complacent.

The oocysts have a hard wall around them, protecting them and making them quite hard to kill. Therefore, choices of cleaning for coccidia are limited to those which can get past that protective wall.

How to Clean for Coccidia

1. Have more than one housing option for the cleaning program.

The program to clean for coccidia is intensive. Maintain a second enclosure throughout the cleaning program if possible. Switch your bearded dragon to the clean cage while cleaning the previously occupied one.

2. Remove or replace cage furnishings and accessories.

To lessen the load on you and increase the chances of success, decide which furnishings your bearded dragon needs in its house and remove the rest.

Anything that is porous or has cracks and crevices will be particularly difficult to clean of coccidia, so it is best removed for now. Any accessories that you are removing will also need to be cleaned before storing. The oocysts can live for years in the right conditions. If the accessories cannot be cleaned, it cannot stay.

Any accessories that can be replaced with disposable items will make your life easier. For example, switch a burrow out for a cardboard box. Alternatively have sufficient accessory replacements that they can be rotated or replaced during the cleaning program period.

Cage accessories such as hammocks may be heat treated depending on what it is made out of. Fabrics may tolerate soaking in boiling water.

Remember that the bearded dragons stress is a factor in coccidia. Ensure your bearded dragon has somewhere to hide. Torn up newspaper in a pile may give some comfort for hiding in to reduce stress while other accessories are missing.

In addition, providing the right lighting and heating setup is critical for health. If you have removed the basking accessories such as rocks and branches, then ensure your bearded dragon can still access the heating and lighting as it chooses for basking.

Bowls should be made of something that will tolerate high temperatures for cleaning.

3. Replace loose substrates and disinfect solid surfaces.

Substrate needs to be solid for effective cleaning, preferably tile or linoleum. Reptile carpets, sand or other substrates that are not easily cleaned in the enclosure (if at all) need to be removed while treatment is in progress or replaced completely daily.

If there are days that you cannot adhere to the cleaning program while clearing up the coccidial infection, then use paper towels or newspaper on the floor surface for those day. Replace the disposable flooring daily. This is not as effective and doesn’t resolve the issue of oocysts spreading further than the floor but should provide better results than doing nothing.

3 of the Best Treatments to Clean for Coccidia

Coccidia is hard to get rid of, those oocysts are super difficult to kill! The oocysts have a hard, resistant wall around them. These strong walls protect the oocysts from harsh environmental conditions prolonging their survival under non-favorable environmental conditions.

Oocysts survive many chemicals and even freezing, but they do not cope with desiccation and high temperatures. With that in mind, here are 3 ways to clean for coccidia including cleaning techniques and products.

1. Heat – Steam Cleaning, Boiling Water and Dry Heat

Using heat to clean for coccidia is the most effective treatment there is and its eco friendly! Steam cleaning your bearded dragons house and accessories is a great option to control the coccidial infection and for regular cleaning going forward.

The steam wand needs to be moved very slowly and methodically around the enclosure walls, moving from top down. The wand will be in very close contact with the walls to get maximum temperature.

Bowls and small accessories can be immersed in boiling water. Leave the accessories in the water until it the water starts to cool.

The oven may also be useful for your bearded dragon’s accessories. The heat and dry air of the oven is quite detrimental to the oocysts. Of course, anything that is intended for the oven needs to be able to cope with the heat and not cause a hazard to you.

It is possible to inactivate or kill coccidia oocysts at temperatures below -30°C (-22°F) or above 40°C (104°F) (Constable, n.d.). Cryptosporidia oocysts will become inactive when exposed to temperatures 45-60°C for 5-9 minutes (Cranfield et al, as cited in Pasmans et al, 2008). Some species will tolerate heat better than others and the duration the heat must be applied for is also variable. So to cover your bases it is better to work with boiling temperature from steam or boiling water.

Needless to say, boiling water reaches 100°C (212°F). To attain that temperature with steam cleaners, the wand will need to be almost in direct contact with the wall. You can test the temperature of the steam by waving the wand over a cooking thermometer.

2. Cleaning products to treat coccidia.

Cleaning products for coccidia are limited. Use a 10% solution of ammonium hydroxide and leave on the areas to be cleaned for at least 45 minutes. Note, when you clean for coccidia, don’t use bleach. Bleach does not kill coccidia (Divers & Mader, 2005).

The protective wall of the oocysts makes them hard to kill with common disinfectants. However, the wall does have tiny pores required for oxygen which some chemicals can get through. Unfortunately, some of those chemicals are quite toxic and you don’t want them in your home.

Ammonia hydroxide is one of the cleaning products that can penetrate the coccidia oocysts wall. Ammonia hydroxide is ammonia with water already added and will come in various concentrations. You may be familiar with cloudy ammonia which is ammonia with soap in it. You need ammonia hydroxide not cloudy ammonia.

Purchase ammonia hydroxide at concentration of 10% or higher. You can dilute higher concentrations to reach the desired 10% for cleaning.

Ammonia is in many household cleaning products; it is alkaline, corrosive and quite suffocating. Regardless of its commonality in our world, take caution and read the manufacturer’s instructions when using. Ammonia is irritating and if inhaled can cause burning of the throat and respiratory tract. It can also irritate the skin, eye and at extremes it can cause burns.

A study back in 1940 by Horton-Smith et al on ammonia concentrations for poultry farming showed that varying concentrations of ammonia and water killed coccidia oocysts over different durations. A 1% ammonia solution killed 100% of oocysts but it took 24 hours whereas a 10% solution only required 45 minutes. Although that was on the Eimeria strain, the strength of ammonia hydroxide solution is echoed by vets treating Isospora strain in reptiles anywhere between 5% (Divers & Mader, 2005) to 10%.

Ammonia hydroxide is an effective cleaning product against oocysts but not effective against most bacteria. To finish off the clean, after treating the coccidia and before you return everything to its place, use a disinfectant such as F10 and dry the surfaces.

3. UV – Sunlight

Can sunlight kill coccidia oocysts? There are a number of studies showing various strains of coccidia will perish in direct sunlight but none specifically for Isospora amphiboluri.

A 100 years ago sunlight was recommended in controlling some strains of coccidia along with hot water and steam (Wilson, 1930). The effectiveness of sunlight killing Eimeria oocysts was also noted by the University of New Mexico Biology (Department of Biology at University of New Mexico, n.d.). In the case of Isospora oocysts Long (Long, 1982) also speaks of unsporulated oocysts being easily damaged if dried out and by direct sunlight.

So, to clean for coccidia use direct sunlight in the cleaning program. Drying accessories in the sun is a good and viable option. Use it as an additional strategy to control coccidia rather than an alternative on its own. There are two problems using it on its own:

  • there isn’t any evidence to show us the effect on Isospora amphiboluri,
  • there are a number of variables such as surface exposure of items, duration of exposure and so on.

However, there is evidence that providing your bearded dragon with that direct sunlight will do wonders for its immune system so it would be good to take it outside as well.

Keep in mind that any accessories with crevices or surfaces that provide cover for oocysts will not be effectively treated by sunlight. Ensure nothing is in between the surfaces that oocysts may have resided on and the sun. No shade, no glass or other objects that may impede the transmission of UV.

5 Steps to Clean for Coccidia in your Bearded Dragon’s House

To clean for coccidia once the infection has taken hold takes a lot of effort. You can apply the following 5 steps to clean for coccidia in your bearded dragons cage as your standard cleaning (just less often) or once the infection has escalated. Prevention is better than cure!

1. Remove and dispose of organic matter.

  • Remove stools as soon as they appear or at the very least, in the morning and afternoon each day. Many oocysts will already be sporulated making them infectious. Remove them and spot clean as quickly as possible.
  • Remove and dispose of any food not eaten on the same day. There is a good chance the food is now infected and cannot be offered again which includes feeders and vegetation.

2. Clean and dry the accessories.

  • Remove and clean food and water dishes. These can be cleaned by immersing in boiling water. Dry in the sun if preferred.
  • Remove and dispose of, or clean, any accessories provided. These can be cleaned with ammonia solution, steam, hot water or other heat method. These can also be dried in the sun.

3. Scrub and disinfect everything.

  • In the enclosure scrub off any residual stool or other organic matter. Organic matter will reduce or void the effectiveness of disinfecting.
  • Clean your bearded dragons house with ammonia hydroxide or steam. Clean anything that could have been touched which includes anywhere fluids could have been flicked.
  • Thoroughly dry the enclosure.
  • If steam was used to clean your bearded dragons cage, then move on to step 4. If ammonia hydroxide was used for cleaning, consider using a disinfectant now to complete the cleaning such as broad-spectrum disinfectant F10. It will do nothing for the oocysts, but it is not intended for them, they have already been treated previously in this step. Follow the manufacturer’s instructions.
  • Thoroughly dry the enclosure again.

4. Replace or restore accessories.

  • Restore the accessories to be used in the enclosure. Provide some form of a hide and basking area at the very least.

5. Clean for coccidia on the cleaning equipment!

  • Clean your cleaning equipment and products the same as you did for your bearded dragons house and accessories. Depending on the piece of equipment you may be able soak it in boiling water, chemical or steam clean.

For bearded dragons clean for coccidia using heat, uv and ammonium hydroxide. The cleaning routine is intensive and spans at least 6 weeks.

See Dr Ahmad’s post on symptoms, diagnosis and treatment of coccidia in bearded dragons for more information.


  • Constable, P. D. (n.d.). Overview of Coccidiosis. Retrieved from MSD and the MSD Veterinary Manual:
  • Department of Biology at University of New Mexico. (n.d.). Biology of the Eimeriidae. Retrieved from UNM Department of Biology
  • Divers, S. J., & Mader, D. R. (2005). Reptile Medicine and Surgery – E-Book. 2nd Ed. Elsevier Health Science.
  • Horton-Smith, C., Taylor, E. L., & Turtle, E. E. (1940). Ammonia Fumigation for Coccidial Disinfection. Veterinary Record, 52, 829-832.
  • Long, P. L. (1982). The Biology of the Coccidia. Baltimore, MD: University Park Press.
  • Pasmans, F., Blahak, S., Martel, A., & Pantchev, N. (2008). Introducing reptiles into a captive collection: The role of the veterinarian. The Veterinary Journal, 175, 53-68.
  • Wilson, I. D. (1930). A study of bovine coccidiosis. Thesis for degree of Doctor of Philosophy. Iowa: Iowa State University Digital Repository.

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