How To Disinfect A Flute At Home: A Guide To Staying Safe!

Closeup of woman playing flute - blowing

While the woodwind instruments may be some of the most delicate and beautiful instruments to play and listen to, they also are some of the most unclean instruments as well. It takes devotion to your instrument and an understanding of proper cleaning and disinfecting etiquette to truly keep these instruments free from the various setbacks that come with a dirty mouthpiece or keys. With bacteria, flus, viruses, and countless transmittable oral diseases all being highly prevalent when it comes to playing woodwind instruments, it’s no wonder why many people are adamant on knowing exactly how to clean their flute to steer clear of all these unfortunate problems entirely.

With the flute specifically, cleaning your headjoint and mouthpiece thoroughly is key but how can you properly disinfect your flute at home, and are there things you should avoid doing to stay safe as well?

The best way to disinfect your flute at home is to use rubbing alcohol or hydrogen peroxide with a cotton ball then let it air dry. Start by dipping the cotton ball in the peroxide or alcohol, rub in a circular motion on the headjoint, body, and foot joints, making sure to get the keys without damaging the pads, and not damaging the cork in the headjoint either. Pay special attention to the mouthpiece and use Q-tips where the cotton balls simply won’t fit. You can also use a cleaning rod and a microfiber cloth, or flute swab, with alcohol on it to clean the inside of your flute as well. 

In order to break this process down further and go over some of the other questions people have when it comes to disinfecting your flute, let’s take a look at the disinfecting process and all it entails in-depth below.

How do You Disinfect a Flute Mouthpiece?

Flute mouthpiece sitting outside of caseWhile disinfecting your keys is important as well, the main thing that you will want to disinfect thoroughly on your flute is the mouthpiece. The mouthpiece is where the most bacteria is found on your instrument and it is also the area you should clean and disinfect after every use without fail.

As we previously discussed in our article Sanitize Your Saxophone Mouthpiece, Neck, and Reed, cleaning your mouthpiece weekly is essential and, with some of the more viral bacterias and viruses going around including COVID-19, it’s no wonder why they now say to disinfect before and after every use.

With this being said, the best way to clean your flute mouthpiece is to use a cotton swab with denatured, isopropyl alcohol on it in order to clean around the embouchure hole first and foremost. Next, you can use alcohol wipes to clean the mouthpiece in between plays as suggested. You can also use a cleaning rod and a microfiber cloth to clean the inside of your head joint thoroughly. Be careful with the cork within the headjoint as water or liquid damage of any kind can shrink and deform this vital part of your flute.

Can You use Clorox Wipes on a Flute?

The next big question that is often asked when disinfecting a flute is whether or not clorox bleach is a good cleaning choice and if the clorox wipes are effective. To answer simply, it is not recommended to use clorox wipes for your flute but you can most certainly use them to clean your hard case.

The reason for this is that bleach is a corrosive chemical that can actually damage your silver flute and damage your headjoint, cork, keys, and pads. Instead, rubbing alcohol and hydrogen peroxide will still remove the bacteria but won’t damage your instrument in the process. However, it is important to note that cleaning your keys with alcohol may dry them out and affect the mechanisms so it is vital that you are careful when doing so. You can use key oil to keep these mechanisms lubricated.

To properly clean your instrument case, another part of the instrument setup that breeds bacteria, use clorox wipes to wipe down the handle thoroughly, the sides and top, as well as the clasps, and inside if possible. You can also wipe down your cleaning rod and other equipment at this time as well.

Can You Clean Your Flute in the Dishwasher?

Let’s be brutally honest for a second: why would you ever clean your instrument in a dishwasher to begin with? Seriously, to truly respect your instrument, you must first think of it as an instrument and not just another chunk of metal that you own. While silverware and silver flutes may seem close to one another at first, the truth is that putting your flute in the dishwasher is sure to be a costly mistake. Why? Well, it’s simple. Your pads and your cork are not meant to experience hot temperatures, water damage, or exposure to soap either. By doing all of the above to them at once, you are subjecting yourself to a pricey situation where all your pads and cork will need to be replaced immediately.

On top of this, dishwashers may be effective for some pieces of metal instruments but the truth is that the heat of your dishwasher could actually warp the intricate metal parts such as the keys of your flute as well. Because keys are not inherently simply or cheap to replace, this could become yet another fiasco caused by the dishwasher cleaning method.

How to Clean and Disinfect the Interior of Your Flute

Wooden flute cleaning rodJust as cleaning the exterior of your flute is important in order to keep your flute clean and disinfected, the interior cleaning process is essential to eliminating bacteria that forms from the vapor of your breath inside the head joint specifically. According to the US National Library of Medicine, “SEM images revealed that most bacteria in exhaled breath are detected in the size range of 0.5–1.0 µm, which is able to enable them to remain airborne for a longer time, thus presenting a risk for airborne transmission of potential diseases.”

In order to eliminate this bacterial growth and to also clean the interior of your flute so as to keep your pads and cork in good condition for longer, you will want to utilize either a cleaning rod or a flute swab. With a cleaning rod, you will need a microfiber cloth and will want to thread the cloth through the cleaning rod hole at the end. Next, you will want to cover the flute rod with the cloth so as to not scratch the flute interior while cleaning. Lastly, use the rod to clean inside the head joint whilst carefully avoiding the cork and repeat the process with the body and foot joint as well. The cloth will absorb the moisture and will remove any bacterial growth that spreads because of it.

Flute cleaning swabWith a flute swab, you will insert the swab string into the head joint and pull through the swab carefully avoiding the cork and letting it soak up the moisture. You can then repeat this process with the body and foot joints. Some will argue that the cleaning rod is a better choice but all in all, the flute swab is better.

In order to stay safe from bacteria and viruses caused by oral vapor specifically, it is best that you disinfect your mouthpiece with alcohol wipes before and after every use and also detach your headjoint and use your cleaning rod or flute swab to soak up the moisture each time.

What can You do if Your Flute Pads or Cork are Damaged?

Perhaps the most sensitive parts of any flute are the cork and the pads. The cork of your flute is located at the very top of your head joint and allows you to separate the pieces. Water damage, heat, and vapor from your breath can all damage this cork over time. The pads are found under the keys of your flute and form a seal over your key holes to allow your instrument to play crisp notes.  Any water damage, heat, dirt, or buildup of cleaning products can destroy these pads entirely.

According to Learn Flute Online, “Do not touch the pads with anything (damage). Look for fraying, peeling, puffing, or tears in the “skin” of the pads. If you see any of these, your flute can limp along for a while, but probably needs repair depending on the severity of the tears. Some bubbling or dirtiness is possibly okay… You can make sure your cork is properly sealing off the end of your head joint by placing the palm of your hand over the opposite end so it makes a tight seal. Next, place your mouth completely over the embouchure hole (where your lips go) and start sucking the air out. Once you have sucked all of the air out your mouth will be vacuum-stuck on there. You can wait a few seconds and then pull off. “Pop” the seal will be broken. If this doesn’t happen, you possibly have a nasty leak.”

With this being said, the best thing to do if you have damage is to simply take it to a local  instrument repair shop and have the pads or cork replaced professionally. When paying as much as you would on flute pads or a cork, the last thing you want is to install them improperly and only make your problem even worse.


Now that you know exactly how to disinfect your flute at home, what cleaning solutions to avoid, and how to handle damage to the delicate parts of your flute, all that is left is to put these tips in practice and stay safe from all viruses and bacteria in doing so. For more information on how to clean wood or plastic instruments such as the recorder, check out our recorder sterilization article today!


An ardant fan of acoustic music, I played the clarinet in high school band and even competed in Disneyland. As the son of a music teacher, I know firsthand the importance of keeping instruments clean and maintained. I now enjoy sharing information with others and providing answers where I can.

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