5 Best Natural (& Effective!) Toilet Bowl Cleaners

By Marilee Nelson |

featured image: 5 Best Natural (& Effective!) Toilet Bowl Cleaners

We know it’s hard to give up chemical cleaners and disinfectants when it comes to toilet cleaning.

After all, most of us are taught the best way to clean our homes (especially our germy toilets and bathrooms) is to nuke those germs using harsh chemicals.

The problem is when we kill germs using disinfectants, like bleach or antibacterial agents, we leave a small amount of those germs behind.

And science has shown that those robust survivors can mutate into superbugs—which you definitely do not want in your home.

Fortunately, there’s a better way to clean your toilets that will remove unwanted germs, stains, and odors without creating superbugs.

This article will share the best natural toilet bowl cleaners and DIY options for a sparkling clean bowl.

Why Switch To A Natural Toilet Bowl Cleaner? 

Chemical-based toilet bowl cleaner is often one of the last products people will give up when detoxifying their homes.

We get it. Toilets can be unpleasant to clean; therefore, you want to make sure to clean them thoroughly.

However, there are several reasons to finally flush that toxic toilet bowl cleaner (figuratively speaking, of course. Please dispose of toxic cleaners safely and legally.).

#1: Toilet bowl cleaner contains a soup of harmful toxins, including sodium hypochlorite or hydrochloric acid, or bleach, which are poisonous if ingested, extremely harmful if inhaled, left on the skin, or splashed into the eyes, and can create toxic fumes if mixed with organic matter, such as urine or feces.

In addition, most toilet bowl cleaners contain endocrine-disrupting chemicals (such as fragrances and detergents) and EPA-registered pesticides.

#2: Toilet bowl cleaners containing antiseptic or antibacterial ingredients, such as bleach, can permanently damage septic systems. They’re also toxic to aquatic life.

#3: Toilet bowl cleaners are responsible for thousands of poisonings per year in people and pets. 

Some side-effects of toilet bowl ingestion, inhalation, or other exposure include: 

  • Organ damage,
  • Trouble breathing,
  • Burning of the throat,
  • Loss of vision,
  • Coma, headaches,
  • Seizures,
  • Blood in stool,
  • and more

#4: Harmful chemicals are not necessary to remove germs and clean a toilet. If there were no other way to clean a toilet effectively, the risks of using synthetic toilet bowl cleaner might outweigh the benefits.

Thankfully, there are plenty of safe and effective ways to clean and disinfect your toilet bowl without subjecting yourself to harmful chemicals.

Ingredients To Avoid In Toilet Bowl Cleaners 

We mentioned a few of these above, but here’s a more comprehensive list of harmful ingredients to avoid in toilet bowl cleaners:

Learn more in: The Most Toxic Cleaning Products To Avoid + Non-Toxic Swaps

The 5 Best Natural Toilet Bowl Cleaners 

What makes these the best natural toilet bowl cleaners?

  • They’re effective on grime, germs, and stains
  • They’re entirely non-toxic
  • They’re eco- and septic-friendly
  • They’re easy to use
  • Their cleaning power lasts longer than a day or two
  • They’re affordable
  • They won’t harm your pets if they drink from the toilet!

Without further ado, here are our top picks for the best natural and effective toilet bowl cleaner substitutes.

1. Branch Basics For Toilets, Bathrooms, And More

Branch Basics is a plant- and mineral-based all-natural, non-toxic, fragrance-free, Made Safe Certified,, septic-safe Concentrate you can use to replace nearly every toxic household cleaner and laundry product..

For toilets, we recommend using Branch Basics Bathroom dilution alone or paired with Oxygen Boost for extra scouring power.

To use:

Step 1: Spray a few sprays of Branch Basics Bathroom in the toilet bowl, on the seat, and around the base.

Step 2: If your toilet is soiled or needs extra cleaning power, add a sprinkle of Oxygen Boost on top of the Bathroom spray.

Step 3: Scrub the toilet bowl and wipe down the seats and base with Branch Basics Bathroom dilution.

Overnight method for stains and deep cleaning: 

Spray Bathroom Spray around the toilet bowl. Sprinkle 1 scoop or more of Oxygen Boost around your toilet bowl before bed. Let sit overnight. 

Scrub lightly in the morning, flush, and wipe down the seat and base using Branch Basics Bathroom dilution or your favorite non-toxic bathroom cleaner.

Learn more in: Non-Toxic Bathroom Cleaning With Branch Basics 

2. Pumice Stones For Stains

Toilet bowl stains resulting from lack of cleaning or hard water are unsightly and can be challenging to remove.

The solution? An inexpensive pumice stone and a pair of rubber gloves. Here’s how.

  1. Clean the toilet using Branch Basics or your favorite non-toxic method.
  2. Put on cleaning gloves.
  3. Using a pumice stone, gently scour the stain until it disappears.
  4. Flush 

Pumice stones can be found anywhere personal care products are sold. 

Just be sure to distinguish between your toilet pumice stone and the one you may use for your feet!

Using a permanent marker to label the stone “for toilets” or adding a dab of non-toxic nail polish and keeping it in your cleaning caddy will usually do the trick.

Discover more time-saving cleaning tools in: Essential Cleaning Tools For A Happy And Healthy Home.

3. Baking Soda + White Vinegar To Clean And Remove Stains

Baking soda and distilled white vinegar are staples among healthy home advocates and DIYers because they work and are cost-effective.

Combining these two in your toilet removes stains, germs, and odors in minutes with minimal effort and zero toxicity.

Here’s how to use baking soda and white vinegar as a natural substitute for toilet bowl cleaner.

Step 1: Flush the toilet to wet the sides of the bowl.

Step 2: Sprinkle baking soda around the bowl.

Step 3: Spray distilled white vinegar on the baking soda (this will create a fizzing effect).

Step 4: Let dwell for 1-5 minutes, depending on the scope of cleaning required. Let dwell for at least 15 minutes for stubborn stains.

Step 5: Scrub with a toilet brush, flush, and you’re done.

Discover more ways to clean with baking soda and distilled white vinegar in:

5. Disinfect Your Toilet Naturally With Hydrogen Peroxide + Vinegar

Although we prefer to remove germs vs. killing them, sometimes using a natural disinfectant is the right course of action ( if sickness is running through your home or you just can’t bear to clean a toilet without disinfecting).

When those times come, turn to this non-toxic method to disinfect toilets, cutting boards, door knobs, and other surfaces.

Research has shown that Vinegar and 3% Hydrogen Peroxide used in combination (in separate bottles) effectively kill germs.

The key is to use them separately and store them in separate bottles. The reason is even though they are non-toxic, they can create harmful fumes if combined.

Materials Needed:

  • Branch Basics Bathroom Cleaner
  • Split fiber Microfiber
  • Distilled White Vinegar (5% acidity)
  • Hydrogen Peroxide (3% solution - brown bottle)
  • A spray nozzle for the brown bottle of peroxide
  • A spray bottle for the vinegar (or a spray nozzle for the bottle if it will fit)

Step 1:

Clean the toilet using Branch Basics or another non-toxic surfactant based soap to remove germs and grime. This is essential because any dirt or matter left behind can interfere with the sanitizing effects of the vinegar and peroxide.

Step 2:

Spray or squirt (hydrogen peroxide bottles work great for squirting directly, and you want to keep your hydrogen peroxide in its brown bottle to preserve it) the surface with one of the liquids. The order doesn’t matter. You can start with either vinegar or peroxide. After spraying, let it sit for 5 - 30 minutes (dwell time), then scrub the bowl with a toilet brush, wipe surfaces with a microfiber cloth, and flush. Remember that vinegar contains acetic acid which is a lung irritant when sprayed.  Refrain from breathing in the fumes from the vinegar when sprayed. It quickly clears if good ventilation is used. Turn on the bathroom exhaust fan and close the bathroom door to clear out the vinegar smell while letting the vinegar dwell.

Step 3:

Repeat with the other bottle by spraying the surface and letting it sit for 5 - 30 minutes (dwell time). Next, scrub the bowl with a toilet brush, wipe surfaces with a microfiber cloth, and flush.

You can use this natural disinfecting/sanitizing method throughout your home as needed.

Learn more in: Is Branch Basics A Sanitizer Or A Disinfectant?

Toilet Bowl Cleaner FAQ’s

We’ve already covered a lot about why you should switch to non-toxic toilet bowl cleaner and the best natural substitutes.

However, there are a few questions left to be addressed. Let’s tackle those now.

Will Vinegar Damage My Toilet Bowl? 

This is one of the most asked questions about using vinegar as a cleaner.

The answer when it comes to toilet bowls is: no. Vinegar will not damage your toilet bowl, tank, or inner components.

On the contrary, it will help clean, disinfect, and prevent hard water damage and corrosion.

You can even leave it on for an extended dwell time without the risk of damage. So, no worries there.

Can I Leave Natural Toilet Bowl Cleaners In My Toilet Overnight? 

Yes! All the toilet bowl cleaning and disinfecting methods listed here can be left on overnight if required (although that’s usually not necessary).

Why Is My Toilet Bowl Stained Brown? 

Brown stains in toilet bowls are usually the result of mineral build-up from calcium, iron, or manganese.

The best ways to prevent this are: 

  • To clean your toilet regularly, like every day or two. 
  • Put white vinegar in your toilet and tank to break down mineral buildup and limescale.
  • Install a water softener and/or water filter to reduce minerals in the water. 

Hard water (water high in minerals) can also affect your drinking water and appliances, such as your dishwasher and washing machine, so it’s worth considering your options.

Can I Use Toilet Bowl Cleaner to Clean My Sink & Shower? 

Normally the answer would be a hard “No! you should never use a chemical toilet bowl cleaner in your shower.”

However, when using a non-toxic toilet bowl cleaner, the answer is an emphatic “yes.”

All the natural substitutes for toilet bowl cleaner shared here can also be used to clean your shower, sink, and the entire bathroom.

Learn more in: Non-Toxic Bathroom Cleaning With Branch Basics 

Try Branch Basics As A Natural Toilet Bowl & Bathroom Cleaner 

We hope this article has inspired you to finally ditch your chemical-based toilet bowl cleaner in favor of non-toxic alternatives.

It may seem like a small thing, but we have experienced and witnessed the incredible health benefits that result from seemingly small acts of tossing the toxins.

Whether you try Branch Basics to clean your toilet or another of these methods, you can feel good knowing you’ve taken a significant step to reduce chemical exposure and create a healthier home.

For more expert tips on detoxifying your cleaning routine, laundry room, kitchen, and more, check Toss The Toxins

Marilee Nelson

Marilee Nelson

Marilee Nelson is an Environmental Toxins expert who has spent nearly 30 years advocating for the chemically-sensitive and chronically-ill. She is a Board Certified Nutritionist, Certified Bau-Biologist and Bau-Biology Inspector and specializes in Food As Medicine. She has helped thousands of families and individuals identify, heal and recover from toxic exposures and is on a mission to revolutionize the way American families view their health.