Citric Acid: The Easy, Non-Toxic Ingredient to Clean Toilet Bowl Stains

You may have been making the switch to natural and non-toxic methods to clean your home, and found plenty of chemical-free ways to do so. But have you struggled to find a natural solution that leaves your toilet sparkling clean and stain-free? What is the best natural cleaner for toilet bowls?

What is the most eco-friendly way to clean a toilet?

Over the years, I’ve tried a LOT of different methods, before finding one that consistently works.

Citric acid!

I now only use citric acid for cleaning my toilets at home, because it is safe, natural, and most importantly – it actually is effective!

Other natural ways of cleaning toilets may work for you, though. It really comes down to just how dirty your toilet is.

No judgements here, on the state of your toilet. I know that for some, a clean toilet is a must in their home, and will scrub it clean daily. Speaking for ourselves – with schedules balancing kids, work and family time – having a sparkling clean house is not always at the top of my priority list. I don’t live in filth. But as long as the everyone is fed, clothes are clean, and the dishes are done – everything else can wait.

As a result, I think it’s fair to say that our toilets were pretty stained, after being left to the bottom of the cleaning priority list (hey I’m not judging you, so please – don’t judge me! 🙂

Don’t misunderstand. It’s not like I never cleaned the toilet. I really do clean my toilets! The problem was always that after I did clean and scrub them, the toilets still looked, well, dirty.

I’m also staunchly against the idea of pouring bleach and other harsh chemicals down the toilet and into the waterways, in pursuit of a pristine toilet. So I simply accepted that a discoloured toilet bowl was something I had to live with, if I wanted to avoid chemicals.

That is, until I finally sat down and got to the bottom of WHY my toilets still looked dirty and stained, after being cleaned. From then on, it was a bit easier to find the best natural way to clean toilet bowl stains. It’s CITRIC ACID, and it will clean the most stubborn of stains plaguing your toilet bowl.

I’m amazed that it has taken me years to find it, as it’s so simple. It’s now my go-to, and now I too am the proud owner of sparkling white toilets. No scrubbing required!

If your toilets need just a light clean, some of the other natural ways to clean toilet bowl stains may work for you. Here is a round-up of the many natural and eco-friendly methods of cleaning toilets that I’ve tried over the years, and how I found them.

If you have tried everything and think your toilet is beyond help (as I did)- please read on to the end, do make sure you try citric acid. It’s the ultimate eco toilet cleaner.

Non-toxic ways to clean toilets

Here are some of the common non-toxic alternatives that you can try for your toilet.

1. Store-bought eco toilet cleaner

Eco-friendly cleaning brands are extremely common now, so it’s pretty easy to find one in a shop. They’re easy to use (usually in a bottle with a bent spout, so you can squirt it under the toilet rim).

The problem is that I have found they’re not THAT effective if you have some bad toilet stains. This won’t be an issue if you clean your toilets super-regularly and don’t let them get too bad.

I have tried Earth Choice (which was OK) but more recently have favoured Ecostore.

Pros: Easy to use

Cons: Expensive (comparatively), and can be ineffective. Best suited for toilets needing a light clean.

2. Coca-Cola

No doubt you have heard about using Coke (or other soft drinks or sodas) being used to clean toilets.

Just pour it into the toilet bowl, leave for a few hours, scrub and then flush!

It works because fizzy drinks contain carbonic acid. That’s how the drinks are fizzy – from carbon dioxide dissolved in water, under pressure. The idea is that the acids in the drink will eat away at toilet stains.

What WON’T work, is using that flat soda water that’s been at the back of your fridge for two weeks. When fizzy drinks are opened, the carbon dioxide gradually gets released, which is why it goes ‘flat’. No carbon dioxide in the fizzy drink, means no carbonic acid. So you are basically pouring just sugar into your toilet.

If you’re going to try this, please try with a freshly opened bottle of fizzy drink.

In my experience, this will do the trick but again – not if you have hard set stains in your toilet.

Pros: Easy.

Cons: Best suited for toilets needing a light clean.

3. Vinegar

Vinegar is an essential in my cupboards, and it is the basis of pretty much how I clean almost EVERYTHING in my house chemical-free. Unfortunately, it didn’t work too well on our badly stained toilets (yeh…they were pretty bad).

While it didn’t do wonders for the toilet bowl stains, I still use it clean the rest of the toilet.

Ways you can use it include:

  • Spraying it on the seat and toilet rim. Leave, scrub, or wipe off with a paper towel. I don’t bother diluting vinegar with water for my household cleaning, as many people suggest. If you don’t like the vinegar smell, rest assured it disappears pretty quickly.
  • Pouring it into the toilet bowl. Leave for a few hours (overnight, even), scrub, then flush. For a boost, try pouring it in with some bicarb soda (baking soda).

Just use the cheap household white vinegar from the supermarket. Don’t go around wasting your fancy apple cider vinegar for this!

Pros: Super easy (most people have household white vinegar). Will be effective for most toilets. It is useful for cleaning all of the toilet (not just the bowl).

Cons: Still not that effective if you have a badly stained toilet.


Citric acid is SERIOUSLY the holy-grail of eco-friendly toilet cleaners.

I don’t have any photos of our toilets prior to my discovery of citric acid. In any case, I’m not so sure I need my toilet shame to be immortalised on the internet until the end of time…

Let’s just say – they were bad. No amount of scrubbing with the toilet brush could make those stains budge. The stains went deep into the U-bend of the toilet (beyond the reach of the brush). Even after I cleaned the toilet, they just still looked infuriatingly unclean.

I once attempted to attack the stains with a disposable chopstick. To my horror, I discovered that those unsightly stains were completely rock solid. Scraping at them did not help. No wonder the toilet brush was futile!

Why do my toilets still look dirty after I clean them?

I reached a point where I decided I’d had enough of our unsightly toilets. Upon realising the stubborn stains were from some serious caked-on stuff at the bottom of my toilet (yes, ew) I had a better idea of what to search for. It was a last ditch effort before I figured the only solution was buying brand new toilets (not exactly cheap or quick).

The more I researched, the more I realised the unsightly mineral deposits staining my toilet were likely limescale.

Many websites suggested simply using soaking the toilet in vinegar as an effective solution for limescale. If you only have a small amount of limescale, this MAY do the trick. Vinegar is generally pretty good for cleaning toilets, but only if they’re a little unclean.

For more stubborn limescale, some have recommended purchasing a cleaning solution called CLR. It’s an acid-based cleaner that treats and removes calcium, lime and rust (hence – CLR. Genius).

CLR is advertised as a ‘safer choice’ to using harsh chemical cleaners. But I’m always a bit wary of products that are hazardous enough to have a safety data sheet, and no clear ingredient list on the packaging. Surely there existed another (more natural) way to clean my toilet bowl of stains?

If your limescale is REALLY bad, the next recommendation I read was to drain your toilet of all water, and to attack it with sandpaper (or um…like an electric grinder?) Yep, you have to get in there and physically SCRAPE it all off.

I’m not afraid of using elbow grease to get things clean, but I must admit the idea of having my arm down the toilet and up the U-Bend with sandpaper didn’t fill me with joy.

But rest assured – there is a better, easier way. It’s CITRIC ACID.

Why is citric acid so effective at cleaning toilets?

You might’ve noticed a common trend amongst all the natural methods for cleaning toilets. It’s usually some type of acid. Vinegar contains acetic acid, Coca-Cola and soft drinks have carbonic acid. If you look at the ingredients of store-bought eco toilet cleaners, there’ll be an acid in there too (Ecostore and Earth Choice both use citric acid).

“So if the store bought cleaners use citric acid, why wouldn’t I just use those, and why aren’t they as effective?”

Good question. The biggest issue with vinegar, soda, or store-bought cleaners, is the strength of the acid. Most of the time, it’s pretty weak. It’s OK for slightly dirty toilets, but if your toilets have serious caked-on limescale, you need some stronger acid.

You can make a decently strong acid at home using citric acid, without having to resort to buying a store-bought acid-based cleaner.

Citric acid is the same stuff that makes citrus fruits sour. But stocking up on lemons, limes and oranges won’t be enough to clean your toilet of serious stains (although it’ll smell divine). Luckily you can buy manufactured citric acid.

How do I use citric acid to clean a toilet?

This is what I do.

Step 1: In a container, dissolve 3 tablespoons of citric acid in some hot water. If it’s the first go and you have real bad limescale as we did, you might need to up the ante and use double that amount.

Step 2: Pour it into the toilet bowl.

Step 3: Leave it there to soak for a few hours. The first time I did it, I left it for about 6 hours.

Step 4: Give it a scrub, and then flush. You won’t need to scrub particularly hard – the acid will literally dissolve most of the limescale and grime. I found most of it came off just from the pressure from the flush.

..and that’s it.

Honestly, the first time I did it I was so astonished I could actually see the bottom of the toilet bowl. There was a bit of limescale remaining, so if that happens then you might need to repeat the process.

After it’s sparkling clean, your next attempts to clean it should be much quicker. You can get away with using less citric acid, and you won’t need to soak it for so long.

Citric acid is the absolute best natural way to clean toilet bowl stains. It’s all I bother using now, apart from some vinegar to spray around the toilet rim.

Where do I buy citric acid?

Citric acid is readily available in most supermarkets. I first bought it to try out in a 75g container from the baking section of the supermarket, for a few dollars.

But if you want to start using it on a regular basis for cleaning, you’ll find you’ll get through that small container pretty quickly.

You can actually buy it for much cheaper, in bulk. I went ahead and sourced myself a 5kg bag of citric acid for all my toilet cleaning.

5kg of citric acid might seem like overkill, but I calculated this will last me YEARS, solely for the purpose of cleaning my toilets.

Also – buying 5kg of citric acid for less than $30, is IMMENSELY cheaper than buying small containers of it from the supermarket. $120 cheaper, in fact.

You should be able to find citric acid in bulk from a soap supplies company, as it’s often an ingredient in soap-making.

In our household, we really do try to stick with natural methods for cleaning. For the longest time we did not have pristine and stain-free toilets, and it felt like the only effective solutions might’ve been to resort to using harsh and toxic chemicals. Which for us, is not a solution at all.

But there ARE natural ways to clean your toilets from stains, and I would recommend citric acid for even the worst of the toilet bowl stains. I really hope this information can be of help to some of you out there. Let me know if you have success!

Because we all deserve sparkling clean toilets.


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