Deep cleaning contact lenses goes beyond the nightly soak most people rely on. It involves physically rubbing the lens surface, using the right disinfection system, and maintaining a clean storage case. Skipping any of these steps leaves behind protein deposits, bacteria, and other microorganisms that a soak alone won’t eliminate. Here’s how to do it properly for both soft and rigid lenses.
Why Rubbing Matters More Than Soaking
Many multipurpose solutions are labeled “no-rub,” but research consistently shows that adding a rub-and-rinse step before soaking dramatically improves disinfection. Studies on non-oxidative multipurpose solutions found that when lenses were simply dropped into solution without rubbing first, infectious organisms were still recovered from the lens surface. Only after rubbing and rinsing were the organisms reduced to undetectable levels. Physical rubbing removes 100 to 1,000 times more microorganisms per milliliter than soaking alone, and it’s the single most effective step for clearing bacteria, fungi, and the parasite that causes Acanthamoeba keratitis.
There’s a direct correlation between the number of cleaning steps you perform and how well your lenses are actually disinfected. The more steps (rubbing, rinsing, then soaking), the better the outcome. Treat the “no-rub” label as a minimum, not an ideal.
The Rub-and-Rinse Method Step by Step
Start by washing your hands with a soap free of moisturizers, lotions, and heavy fragrances. These ingredients can leave a film on your fingers that transfers to the lens surface. Dry your hands with a lint-free towel.
Place the lens in the palm of your hand and apply several drops of your cleaning solution. Using one fingertip, gently rub both sides of the lens for about 20 seconds. For soft lenses, use a light back-and-forth motion rather than a circular one, which can tear the edge. Then rinse the lens thoroughly with fresh solution, never tap water, and place it in a clean case filled entirely with new solution. Let the lenses soak for the time specified on the bottle, typically six to eight hours.
If you consistently work with the same eye first each time, you’ll avoid accidentally swapping your right and left lenses.
Hydrogen Peroxide vs. Multipurpose Solutions
Hydrogen peroxide-based systems are a step up in disinfection strength. They work by oxidizing organisms on the lens surface, then neutralizing into saline over a required soak period of six to eight hours. You place the lenses in a special case with a neutralizing disc or tablet, fill the case with the peroxide solution, and leave it alone. Never put a peroxide solution directly in your eye: it must fully neutralize first, or it will cause intense burning and pain.
These systems are preservative-free once neutralized, making them a good choice if your eyes are sensitive to the preservatives in multipurpose solutions. They also eliminate the risk of “topping off,” a habit the CDC found in 55% of contact lens wearers, where old solution is left in the case and new solution is poured on top. Topping off dilutes the disinfectant and lets biofilm build up. With peroxide systems, you use the entire vial of solution each time.
One important rule: don’t mix different brands or types of solution. Combining two products can double your exposure to a particular preservative or introduce an ingredient that irritates your eyes.
Cleaning Rigid Gas Permeable Lenses
Rigid (GP) lenses require a slightly different routine because they use different materials and accumulate protein deposits more visibly over time. After removing a GP lens, place it in your palm, apply several drops of a dedicated GP cleaner, and rub each side for 10 to 15 seconds. GP cleaners tend to be more abrasive than soft lens solutions to handle the harder surface.
Rinse the lens with a GP-compatible multipurpose solution or saline. Then place it in the case and submerge it fully in a conditioning or soaking solution for at least four to six hours. Some GP wearers use separate products for each step: a cleaning-only solution (typically sold with a red cap) for rubbing, and a separate soaking and conditioning solution for overnight storage. Cleaning-only solutions are not safe to go directly in your eyes, so thorough rinsing afterward is critical.
For stubborn protein deposits, enzymatic cleaners can be added to your soaking solution. Depending on how quickly deposits build up on your lenses, you might use an enzymatic cleaner weekly, biweekly, or monthly. These cleaners break down protein but not lipid (oil-based) deposits, so they complement daily rubbing rather than replacing it.
Never Use Tap Water
Tap water is one of the most common sources of serious contact lens infections. About 10% of tap water samples in one study tested positive for Acanthamoeba, a parasite that causes a rare but devastating corneal infection. Nearly 90% of Acanthamoeba keratitis cases are linked to contact lens wear, and the specific risk factors include rinsing lenses with tap water, washing the lens case with tap water, handling lenses with wet hands, and even washing your face while wearing lenses.
Older buildings and properties served by rooftop water tanks carry a higher contamination risk. The bottom line: sterile saline or your recommended lens solution are the only liquids that should touch your lenses or case. This applies to GP lenses as well. While rinsing GP lenses with tap water is still technically FDA-approved, most lens manufacturers and solution labels advise against it, and tap water should never be the last thing on a lens before it goes in your eye.
How to Clean and Replace Your Case
Your lens case is just as important as the solution inside it. Poor case hygiene allows biofilm, a slimy layer of bacteria, to coat the interior surfaces. Once biofilm forms, even fresh solution can’t fully disinfect what’s stored inside.
After inserting your lenses each morning, dump out all remaining solution from the case. Rub the inside of each well with clean fingers and rinse with fresh solution (not water). Then leave the case open and upside down on a clean tissue to air dry completely. Moisture left in a sealed case between uses creates the exact environment bacteria thrive in.
Replace your case every three months. Even with daily cleaning, cases accumulate contamination over time that you can’t see. Most solution bottles come with a new case, so swap it out each time you open a new bottle.
Automated Lens Cleaners
Ultrasonic and vibrating lens cleaners are marketed as a hands-free alternative to manual rubbing. The evidence on these devices is mixed. Early studies on ultrasonic units found only minimal reduction in microorganisms even after 22 minutes of operation. Newer vibration-based devices perform better, generating multidirectional agitation that enhances the effectiveness of whatever solution you’re using. These devices can be helpful for people with dexterity issues or who struggle with manual cleaning, but they work best as a supplement to proper solution use, not a replacement for the full cleaning regimen.
Common Mistakes That Undermine Deep Cleaning
A 2014 CDC survey found that half of all contact lens wearers had slept in their lenses, and more than half topped off their solution rather than replacing it fresh each time. Both habits significantly raise infection risk. Other common pitfalls:
- Reusing solution. Solution loses its disinfecting power after one use. Always empty the case and refill completely.
- Skipping the rub step. Even with “no-rub” solutions, mechanical rubbing removes far more deposits and organisms than soaking alone.
- Storing lenses in water or homemade saline. Neither is sterile, and both allow dangerous organisms to survive.
- Wearing lenses past their replacement schedule. No amount of deep cleaning can restore a lens that has exceeded its intended lifespan. Deposits accumulate within the lens material itself over time.
- Showering or swimming in lenses. Water exposure from any source introduces Acanthamoeba and other pathogens directly to the lens surface.