SOP for Cleaning Microbiology Incubators

In short: This is an illustrative cleaning SOP template for incubators used by a pharmaceutical microbiology quality-control laboratory. Adapt it to each unit’s approved instructions, laboratory risk assessment, and controlled cleaning programme before use. The inherited weekly frequency and unnamed disinfectants need site confirmation.

Objective

Describe a controlled method for cleaning the chamber and removable racks of microbiology laboratory incubators while protecting cultures, the equipment, and test work from mix-ups or contamination.

Scope

This example applies to incubators used in a pharmaceutical microbiology QC laboratory. It does not set a cleaning agent, dilution, contact time, cleaning frequency, or temperature limit. Follow the current instructions for the specific incubator model and the laboratory’s approved procedures.

This template is limited to incubators. Refrigerators are not covered; the site must decide whether they belong in scope and establish equipment-specific instructions for them.

Responsibilities

Example in-house criterion (not a pharmacopoeial requirement): A trained microbiologist or authorised designee performs and records the cleaning. The Head of Microbiology ensures that the local procedure, training, materials, and review arrangements are approved and effective.

Procedure

Frequency and preparation

Example in-house criterion (not a pharmacopoeial requirement): This example SOP proposes cleaning weekly. Set the actual interval in the site’s controlled programme using the equipment instructions, intended use, risk assessment, and relevant environmental-monitoring results. WHO guidance calls for a documented cleaning and disinfection programme and consideration of monitoring results, but it does not prescribe a universal weekly interval.

Before starting:

1. Check the incubator identity and status. Confirm that cleaning is due and that no maintenance, alarm, deviation, or open investigation makes the unit unavailable for routine cleaning.
2. Identify the cultures, media, or other items in the unit. Move, protect, or otherwise handle them only under the applicable approved laboratory procedure; do not leave test material at an uncontrolled condition.
3. Gather the approved cleaning materials and the site-authorised disinfectant. Check their identity, preparation, expiry or in-use status, and the instructions applicable to the intended surface.
4. Protect the chamber’s sensors, controls, electrical parts, and other components as directed by the equipment manufacturer. Do not spray or apply liquid directly to these parts unless the instructions explicitly allow it.

Cleaning the chamber and racks

Example in-house criterion (not a pharmacopoeial requirement): Use a clean, non-shedding sponge or cloth only if it is approved for the incubator’s interior surfaces. Follow the manufacturer’s permitted method for removing removable racks and cleaning the chamber. Do not use abrasive materials or chemicals that could damage the unit.

1. Follow the model-specific safe shutdown procedure if cleaning requires the unit to be switched off. This example mentions switching off the main switch; apply that step only where the site has confirmed it is safe for the specific model and its current load.
2. Remove or reposition racks only as permitted by the manufacturer. Clean the interior surfaces and racks with the approved cleaning method, working from cleaner to more soiled areas and changing materials when they are visibly soiled.
3. If disinfection is required by the approved local procedure, apply the selected agent to the permitted surfaces and observe its approved contact time. Rinse or dry only when the equipment instructions or product label require it. Keep solutions away from protected components.
4. Refit racks and accessories correctly. Check that no cleaning material, residue, or loose item remains in the chamber.
5. Restore the incubator to service using its approved startup procedure. Confirm and record that its displayed operating condition is within the established, approved setpoint and acceptance criteria before returning test material. Do not create a new limit in this SOP.

This example names “DISINFECTANT 1” and “DISINFECTANT 2” but gives no product, preparation, contact time, or reason for alternating them. Treat those names as placeholders, not directions for use. Use only products listed in the approved site procedure and compatible with the equipment and work.

Records

Example in-house criterion (not a pharmacopoeial requirement): Enter the cleaning date and time, incubator identification, work performed, materials or approved agent used, any observation or problem, and the performer’s identity in the controlled equipment log. Record deviations and equipment status under the site’s relevant procedures. WHO TRS 961 Annex 2 §§4.1 and 4.3.4 discusses equipment records and monitoring incubator operating temperature; EudraLex Chapter 4 §4.31 describes chronological logbook entries that include cleaning operations and the people who performed them.

Retain batch-specific GMP records at least one year after expiry of the respective product batch. Under EU GMP Part I Chapter 4 §4.11, batch documentation is retained for one year after expiry or at least five years after Qualified Person certification, whichever is longer. 21 CFR 211.180(a), current eCFR (2026), also sets at least one year after expiry for production, control, or distribution records specifically associated with a drug-product batch; retain records longer when applicable law or the marketing authorisation requires it.

Related procedures

• Good microbiological laboratory practice
• Cleaning glassware used in chemical and instrument analysis
• Disposal of QC laboratory waste

Frequently asked questions

Is weekly cleaning a regulatory requirement?

No universal weekly schedule is stated in the cited WHO microbiology-laboratory guidance. The site’s approved frequency should be justified for its equipment and use and reviewed against relevant monitoring information.

Can any disinfectant be used inside an incubator?

No. Use only a product and method approved for the specific incubator surfaces and laboratory use. Follow the applicable product label and equipment instructions, including any required contact, rinse, or drying steps.

When may the incubator be used again?

Return it to service only after the approved restart checks are complete and its operating condition meets the site’s established acceptance criteria. WHO TRS 961 Annex 2 §4.3.4 says incubator temperature characteristics should be established and documented and that operating temperature should be monitored with records retained.

References

1. World Health Organization. WHO good practices for pharmaceutical microbiology laboratories, WHO Technical Report Series No. 961, Annex 2 (2011), §§2.3.1–2.3.2, 4.1 and 4.3.4. Official WHO PDF.
2. European Commission. EudraLex Volume 4, EU Guidelines for Good Manufacturing Practice, Part I, Chapter 4: Documentation (January 2011), §§4.11 and 4.31. Official PDF.
3. United States Electronic Code of Federal Regulations. 21 CFR §211.180(a), current eCFR edition (2026; accessed 19 October 2026). Official regulation.