How to Efficiently Deep Clean Your Smelly Bathroom [Step By Step Checklist]

You follow a weekly cleaning routine, but you still can’t seem to get rid of that moldy, musty pee smell. Here’s a bathroom deep clean process that will ensure you disinfect every surface and eliminate all of those nasty smells in the process.

You’ve cleaned around the toilet several times, but nothing seems to help. Maybe it’s time to give your entire bathroom a super deep cleaning.

I deep clean mine during my regular spring cleaning, but I also like to do it about once a month just because of how dirty it can get. This process is the most efficient way I’ve found to get it done. You can see the other processes I use on my cleaning page.

Related Article: Dirtiest things you should be cleaning but aren’t

Difference Between Deep Cleaning and Weekly Cleaning?

During a weekly cleaning session, you primarily concentrate on flat, visible, surfaces. You give each surface a quick wipe down and call it good. This is a weekly maintenance type clean and not meant to replace the deep cleaning.

During a deep cleaning (spring cleaning) session, you’ll clean every nook and cranny including under and behind fixtures, and inside cabinets and cupboards. It’s all laid out step by step in the deep clean bathroom checklist below.

Clean tub, sink and toilet in a marble master bathroom

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How Long it Takes to Deep Clean a Bathroom With This Process?

The amount of time it’ll take to deep clean a bathroom with this process can vary greatly depending on several factors including the size of your bathroom, how dirty it is, how many people use it and how often you clean it.

My bathroom is fairly small and only used by two people on a regular basis. I do a 30-minute surface cleaning routine every week.

Following my step by step process to deep clean my bathroom usually takes me approximately 60 minutes. Some of that is ‘wait’ time for the cleaner to work.

Related Article: Deep clean your bedroom like a pro


weekly cleaning checklist on a tablet

Join thousands of VIPs for cleaning, decluttering, and organizing tips sent straight to your inbox. As a welcome gift, we’ll send you this FREE printable Weekly Cleaning Checklist that lists exactly what to deep clean in every room of your home.

How Often You Should Deep Clean your Bathroom

How often you deep clean your bathroom using the deep cleaning checklist depends on the same factors as above. You’ll need to decide what frequency works best for your family, but if you notice a musty, moldy, or urine smell, it’s probably a good time for a deep clean.

I typically try to deep clean my bathroom once a month, but I make certain I follow this process in April as part of my spring cleaning routine, and in November to get my home ready for the holidays.

Quick note, if the counters and cabinets are cluttered, declutter your bathroom before deep cleaning so you aren’t cleaning things that don’t shouldn’t even be in there.

1. Gather Your Supplies – 5 minutes

I keep cleaning kits in the major areas of my house, so I already have most of these supplies in a bin under the bathroom sink. Here’s a list of the ones I use.

  • Microfiber Mop or Duster – I use a microfiber mop, but you can use whatever you like for dusting.
  • Vacuum Cleaner – You’ll want a vacuum with a wand at upholstery attachment. I use a Shark Professional.
  • Stiff Bristle Brush – I use a paintbrush and grout brush.
  • Toilet Cleaner – Use your toilet cleaner of choice. Over the years, I’ve found that ‘The Works” performs best and is also handy for cleaning really dirty grout.
  • Toilet Brush – You can use any toilet brush that’ll fit in the bowl and tank of your toilet. I use the disposable ones so I don’t have to worry about cleaning the toilet brush too.
  • Tub and Shower Spray – I personally like using Scrubbing Bubbles when deep cleaning my bathroom. It seems to work a lot better than some of the other cleaners I’ve tried including the baking soda, vinegar, and Dawn concoction.
  • Scrubber Sponge – You’re going to want to have a good scrubber sponge for getting all fo the shower scum and buildup off of the shower.
  • Glass or multi-surface cleaner – Use any cleaner you like, but I find that Hopes Miracle multi-surface cleaner works best for me.
  • Microfiber Cloths – You’ll need several microfiber cloths. I prefer to use colored ones so I can keep track of which cloth is for which mess.
  • Canned Air – My cleaning secret weapon. You can use a small steam cleaner instead if you have one.

2. Empty Storage Areas – 5 minutes

Remove everything from any shelves, drawers, and cabinets. I place all of mine in a laundry basket in the middle of the bathroom so it gets steamed with the rest of the bathroom for easier cleaning.

3. Throw All Linens in the Washer – 5 minutes

Remove any towels, shower curtains, rugs, bath mats, or window coverings and throw them in the washer for a good sanitizing wash.

If you store your towels in the bathroom, go ahead and throw them all in the washer too. This gets them out of your way and they can always use a good sanitizing wash to keep them fresh and fluffy.

To get the towels super soft, throw in 1/2 cup of baking soda with your laundry detergent, you’ll be surprised at the difference it makes. And never use fabric softener on your towels, because it will actually make them repel water instead of soaking it up

4. Remove Dust Buildup From All Surfaces – 10 minutes

Towels and toilet paper create a lot of dust and lint due to how often we use them. Vacuuming the surface dust will make cleaning the rest of the bathroom easier since the dust particles won’t be mixing with the moisture and your cleaners.

Exhaust Fan

A large portion of dust particles get sucked up into the exhaust fan. Combine that with the moisture in a normal bathroom, and you’re going to get a lot of buildup on that fan.

Remove and vacuum the fan vent cover, then put it in the sink. Vacuum the fan motor and use a paintbrush to loosen and vacuum as much of the buildup as possible.

If you follow our weekly cleaning schedule, you’re already vacuuming the fan cover once a week, but that doesn’t take care of the buildup that gets on the fan motor and mechanisms behind the cover


Remove and vacuum any light fixture covers and place them in the sink if possible. Don’t forget to dust the light bulbs.

If you choose to use a duster for this step, use caution around hot lightbulbs because they can melt the duster depending on what material it’s made of.

Flat Surfaces

Use a duster or microfiber mop to dust the ceiling, walls, tops of cabinets, mirror frames, shower surround, shower head, and tub surround. I use a microfiber mop on the ceiling and walls, and a microfiber cloth on the rest.


Close the blinds and or window coverings and vacuum one side, then close them the other way and vacuum the other side. Vacuum the window and any debris in the window tracks.

Shelving, Cabinets, Counters, and Drawers

Vacuum up any loose dust and debris from shelving, cabinets, countertops, and drawers.


Vacuum any remaining dust and debris off of the floor.

5. Apply Cleaners – 5 minutes

Most cleaners work better when they have time to sit and attack the dirt and grime, so I suggest applying all of the cleaners and turning on the hot water to steam up the bathroom.

Toilet Cleaner

Shut the water supply to the toilet off, then flush the toilet to drain the tank and toilet bowl.

Apply toilet cleaner or some hydrogen peroxide to the underside of the toilet rim, all around the inside of the bowl, and around the insides of the toilet tank. Leave the tank lid off and the toilet seat up.

Shower and Tub Cleaner

Apply the shower and tub cleaner or straight hydrogen peroxide to the sink, showerhead, shower walls, tub walls, and around the base of the toilet.

Multi-Surface Cleaner

Next, spray your multipurpose cleaner on the mirrors, window tracks, faucets, outer shower door, outside of the toilet, and any other fixtures. I also spray it on any shelving, and in any drawers and cabinets.

Walk away and let the cleaners work for 15 minutes or so.

6. Steam Up the Bathroom – 10 minutes

Fill the sink with enough water to cover the vent cover and any lighting fixture covers you removed earlier.

Turn the shower on hot and close the shower and bathroom doors. Let the room steam up for approximately 10 minutes. The steam will help the cleaner penetrate and loosen and caked-on mess.

clean bathroom with teal walls

7. Deep Clean the Bathroom – 20 minutes

There’ll be a lot of moisture in your bathroom at this point, so you might want to flip the breakers and interrupt the power while you clean anything that is powered by electricity. I do those things first and use a battery-powered spotlight if it isn’t light enough to see.

Clean Fan, Outlets & Switches

Using your microfiber cloth and a stiff brush, wipe down the fan motor and mechanism. It should be pretty clean from being dusted, but this will remove any remaining buildup that was loosened by the steam.

Next, clean the crevices around all electrical outlets and switches. After loosening the gunk, you might need to give it a quick spray with the canned air to blast out any crud.

Before you turn the breaker back on, wipe down the light bulbs and lighting fixtures while they are cool, then you can turn the breaker back on.

Clean the Shower and Tub

Use your scrubber sponge to clean the tub, showerhead, faucets, walls, floor, and doors.

If your showerhead has limescale or hard-water buildup, you can cover it with a bag full of vinegar and let it soak overnight, then remove and scrub.

If you have stubborn mold, spray it with hydrogen peroxide, let it sit for 15 minutes, then scrub and rinse.

Clean the Blinds, Window, and Tracks

Wipe down the slats of the blinds with a microfiber cloth and pull them completely open so they’re out of the way.

Clean the window tracks and use the stiff brush and canned air to remove any remaining gunk. Read more about this window track cleaning hack here. Wipe down the window and frame.

Clean Fan Cover, Lighting Fixtures, and Sinks

Wash, rinse, dry, and replace the fan cover and lighting fixtures covers. Scrub, rinse, and dry the sinks and faucets.

Clean Flat Surfaces

Wipe the ceiling and walls down with a microfiber mop or cloth. I use a microfiber mop because it goes much quicker.

Use a microfiber cloth to wipe down your vanity, mirror, mirror frame, countertops, and the exterior and interior surfaces of any cabinets and drawers.

Scrub the Toilet and Surrounding Surfaces

Scrub the inside of the toilet tank and toilet bowl, then turn the water back on to fill and rinse. If you have stubborn buildup or stains in your toilet, use a pumice stick to clean it off. The pumice is abrasive enough to remove the buildup, but won’t scratch your toilet.

If you aren’t using a disposable toilet brush, make sure to disinfect your toilet brush when you’re done using it.

Use a grout brush to scrub around the toilet lid bolts and around the base of the toilet. These are the places that collect hidden gunk and part of the reason when your bathroom gets smelly.

When I’m done scrubbing, I use a shot of canned air to blast the gunk out. I buy very specific toilet seats because the bold design is easier to clean and has less room for the nastiness to collect and hide. The plastic ones are the worst.

Next, wipe down the entire exterior surface of the toilet including the water lines, you’ll be surprised how much gunk collects on those lines. Last but not least, wipe down the walls and any cabinets surrounding the toilet.

FYI – If you ever flush your toilet with the lid open, a large cloud of teeny tiny toilet water drops and whatever else you just deposited, can spray up to six feet high. Gross – right! And where is your toothbrush?!!

Related Article: Dirtiest places you’re forgetting to clean

Clean Floor

Working your way from the farthest corner to the door, clean the flooring surface with your tool of choice. I use my Shark steam mop when I’m doing the deep clean.

Deep Clean Bathroom Checklist Complete

Congratulations! You completed the checklist and now have a fresh, sparkling clean bathroom. Add it to your deep cleaning routine and never worry about pee smell again.

Bonus Tips for Deep Cleaning the Bathroom

  • Treat your fixtures, shower walls, and doors with car wax or RainX to help repel water stains.
  • Use The Works toilet cleaner to tackle super dirty grout.
  • Clean moldy sealant by covering and soaking with a bleach soaked cotton beauty coil.
  • Use a black light to find hidden urine.
  • Use hydrogen peroxide to disinfect surfaces.
  • Treat your fixtures with car wax or wax paper to help repel water spots.
  • Canned air or a steam cleaner makes cleaning around the toilet seat bolts and bottom of the toilet bowl easier. It can also be used for the window and shower tracks.
deep cleaning the bathtub

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  1. Alicia Hursley says:

    The fan cleaning tips are a game changer haha I feel like we can actually breathe a little easier now and our bathroom also feels far less humid. Thanks for sharing the tips. To add on a little, I think getting tile and grout professionally cleaned at least once a year is really important. The pros know how to eliminate bacteria better than we average folk.

    1. It’s amazing how much all of that lint and dust can clog up your fans.

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