If you’ve ever walked past our loading dock and seen a stack of used biochemical incubation equipment heading back to our service bays, you know how often this question comes up: how do you properly clean and maintain this gear? As a biochemical incubation equipment supplier, I spend every day working with labs from high school classrooms to pharmaceutical R&D facilities, and the one thing all of them have in common is that even the most advanced incubators and shakers won’t deliver reliable results if they’re not cleaned right. I’ve seen a new incubator return with three failed cell culture runs because a technician skipped a quick wipe-down after a yeast contamination event. I’ve watched a shaker’s motor die early because spilled buffer wasn’t cleared from its base. Cleaning isn’t just a chore—it’s part of protecting the investment you made in your equipment, and it’s also how you get consistent, reproducible data that you can actually trust. Today, I want to break this down step by step, share the mistakes I see all the time, and give you a routine that works for every type of incubation equipment we supply, from compact benchtop models to large floor-standing incubation rooms. Biochemical Incubation Equipment
First, let’s get one thing straight: not all biochemical incubation equipment is the same, and neither are the contaminants you’re cleaning. An incubator for mammalian cell culture has to handle completely different gunk than a microbial fermentation incubator, a CO2 incubator, or a shaking incubation system. Mammalian cultures leave behind dead cell debris, serum residues, and sometimes trace amounts of antibiotics or growth factors. Microbial incubators get coated in yeast mats, bacterial biofilms, and spilled broth. Shaking incubators have spills from T-flasks, centrifuge tubes, and cell culture media that can seep into the moving parts, causing corrosion or jamming. That’s why the first rule of cleaning is to tailor your method to what your incubator is being used for. I always tell new customers to label each equipment unit with its primary use, so you don’t accidentally use a harsh cleaner on a surface that’s supposed to stay chemical-free for sensitive assays.
Let’s start with the pre-cleaning step, something almost everyone skips, and it sets the tone for how well the rest of the process works. Before you take any cloth or cleaner to your incubator, you have to power it down and disconnect it from the power source. This isn’t just a safety thing—though it’s a non-negotiable if you’re working near electrical controls in humid or wet conditions—it also lets the unit cool down if it’s been running at incubation temperature, which prevents sudden temperature changes from damaging sensitive components like gaskets or temperature sensors. Next, remove all removable parts: shelves, trays, doors, gasket seals, sample racks, and even the drip trays that catch spills. I’ve seen labs leave drip trays full of old media for weeks, and by the time they take them out, they’re growing their own microbial culture inside your incubator. Take these parts to a dedicated cleaning sink, not the one you use for glassware or hand-washing, and don’t let any of them touch the bench where you prepare sterile samples later—contamination is a two-way street here.
Now, the most important part: choosing the right cleaners, and learning what not to use. This is where I see the most mistakes. A lot of people grab the first household disinfectant they have under their sink, thinking more powerful equals better. But household bleach, ammonia, and window cleaners have harsh chemicals that can leave residues on incubator surfaces. Those residues will leach into your next culture, alter pH levels, or even kill your cells before they start growing. For general, low-level contamination on stainless steel interior walls and removable parts, I recommend a mild, pH-neutral laboratory detergent. These are gentle enough to not leave residue, but strong enough to cut through serum residues, dried media, and light biofilms. For stubborn spots, like a dried yeast mat on an incubation tray, you can make a 70% ethanol solution—this is safe for most surfaces, evaporates quickly, and doesn’t leave a residue. The only time I use a stronger disinfectant, like a 10% bleach solution, is if there’s a known contamination event—like mold, or a bacterial strain that’s resistant to regular cleaners. Even then, I warn customers to rinse those surfaces thoroughly with sterile water after, because bleach can damage plastic gaskets over time. The big no-no? Never use abrasive scrubbers like steel wool or scouring pads on stainless steel interiors. They leave tiny scratches that trap bacteria and make future cleaning harder. Stick to soft microfiber cloths or non-abrasive nylon sponges—they do the job without damaging the surface.
Let’s walk through the cleaning process for specific equipment types, because that’s where generic guides fall flat. Let’s start with benchtop incubators, the most common units in small labs and classrooms. For these, after removing all the parts and powering down, first wipe the interior walls, top, and back with a damp microfiber cloth soaked in mild detergent solution. Pay extra attention to the corners where shelves meet the walls, and the area around the temperature sensor—this is where spilled media often pools, and if you miss it, it can cause false temperature readings. Once you’ve wiped the interior, rinse the cloth with clean water and go over the surfaces again to remove any detergent residue. Then, clean all the removable parts: trays, shelves, and gaskets. Gaskets are super important—they create the airtight seal that keeps temperature and humidity stable, so if they’re dirty or cracked, your incubator won’t perform right. Wash gaskets with the same mild detergent, being careful not to twist or stretch them, because that can ruin the seal. Dry all parts completely with a lint-free cloth before putting them back in—moisture left in the unit can lead to mold growth between uses.
Next, floor-standing incubation shakers, which are used for everything from microbial cultures to protein expression. These have moving parts, so cleaning them needs a little extra care. After powering down, first check the base of the shaker for spilled buffer or media. I can’t tell you how many times we’ve repaired a shaker motor because a customer let a 50mL tube of LB broth leak into the base. Use a damp cloth (not soaking wet) to wipe down the base, and never spray liquid directly into the motor compartment—use a small brush to gently remove any debris from the vent slots instead. For the shaking platform, clean it the same way as an incubator tray: mild detergent, rinse, dry, and make sure all the tube clamps and holders are free of leftover media. If you use sterile flasks on your shaker, you can even wipe the platform with 70% ethanol before placing new flasks to add an extra layer of protection.
What about CO2 incubators, which are used exclusively for mammalian cell culture? These are the most sensitive, because even a tiny residue can ruin an entire cell line. For CO2 units, after powering down, first remove the water pan at the bottom that maintains humidity. Wash this pan with warm soapy water, and if you have mold growing in it (which is common if you don’t change the water weekly), add a small amount of citric acid to the water when you rinse it—citric acid dissolves lime deposits and kills mold without leaving residue. The interior walls of a CO2 incubator should be wiped with a mild, non-ionic detergent, followed by a rinse with sterile water, because even regular tap water has mineral residues that can build up over time and affect pH. The HEPA filters on CO2 incubators are another important part—check them every three months, and if they’re dirty or clogged, replace them. A clogged filter makes the incubator work harder, which shortens its life, and it can also circulate contaminants around the unit.
Now, let’s talk about routine maintenance, because cleaning isn’t just a deep clean once a month. The best way to keep your equipment clean is to do small, regular tasks that prevent big messes. I tell all my customers to do a quick 5-minute wipe-down after every use: wipe up any spills immediately, remove any used flasks or plates, and wipe the door gasket to make sure there’s no crumb or media residue. Once a week, do a more thorough wipe of the interior, clean the drip tray, and check the gasket for damage. And once a month, schedule a deep clean, which is when you remove all shelves, gaskets, and water pans, clean each part thoroughly, and let the incubator run empty for an hour at 60°C (140°F) to kill any remaining microbes—just make sure you don’t have any plastic parts in there that can’t handle high temperatures.
I also want to share the mistakes that I see labs making that end up costing them time and money. The first is waiting too long to clean. I had a customer call me last year, panicking because their incubator’s temperature reading was off by 3 degrees. When we opened it up, there was a thick layer of dried yeast on the back wall, which was blocking the sensor. They said they’d been meaning to clean it for two weeks, and that small inaction ruined three yeast cultures and cost them a week of work. The second mistake is mixing cleaning supplies. Some people use bleach, then immediately use ethanol to disinfect, and that combination creates toxic fumes that can not only be bad for you but also leave residues on equipment. Always use one cleaner at a time, rinse thoroughly, and wait before switching to another. The third mistake is ignoring calibration alongside cleaning. After you clean your incubator, take two minutes to check the temperature and CO2 readings with a calibrated thermometer and CO2 sensor. Cleaning can sometimes knock sensors out of alignment, so verifying that your equipment is working correctly after you clean it is just as important as the cleaning itself.
Laboratory Analytical Instruments At the end of the day, your biochemical incubation equipment is an investment, and proper cleaning is how you protect that investment. When you keep your incubators, shakers, and CO2 units clean, you get consistent data, fewer contamination events, and longer equipment life—all of which save you time and money in the long run. If you’re not sure about the right cleaner for your specific unit, or if you need guidance on creating a cleaning schedule that fits your lab’s workflow, don’t hesitate to reach out. We’ve helped hundreds of labs optimize their maintenance routines, and we’re here to answer any questions you have about keeping your equipment running smoothly. If you’re looking to upgrade your incubation equipment or replace units that are past their prime, we can also walk you through our product lines and help you find the units that will work best for your specific applications.
References
- American Society for Microbiology. (2011). Guidelines for the Cleaning and Disinfection of Laboratory Equipment and Surfaces. Applied and Environmental Microbiology, 77(15), 5187–5198.
- World Health Organization. (2016). Laboratory Biosafety Manual, 3rd ed. WHO Press.
- FDA. (2019). Good Laboratory Practices for Industry. U.S. Food and Drug Administration.
- CLSI. (2005). Laboratory Decontamination and Sterilization in the Health Care Setting; Approved Guideline. Clinical and Laboratory Standards Institute.
Hebei Wanluda Testing Instrument Equipment Co., Ltd.
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