There comes a morning in late September when the greenhouse stops being a growing space and starts being a shed. The tomatoes are stringy, the cucumber has given up, and the floor is a drift of dead leaves and dried-out modules. It is tempting to shut the door on all of it until March.
Don't. Almost everything that goes wrong in a greenhouse next spring is already living in it right now. Red spider mite is crawling into the frame joints to hibernate; whitefly scales are sitting on the undersides of the leaves you have not pulled; botrytis spores are settling into that pile of dead foliage. An autumn clean is not housekeeping — it is the single most effective pest and disease control of the whole year, and it takes an afternoon.
- Best time late September–October, once summer crops finish
- Why now overwintering pests, fungal spores, and scarce winter light
- Kit hot soapy water, stiff brush, plastic plant label, disinfectant
- Time needed half a day for a typical 6 × 8 ft greenhouse
Why autumn, and not spring
Most gardeners clean in March, on the first warm weekend, with a tray of seedlings already waiting. By then it is too late to matter. Red spider mite females change colour in autumn — from pale green to a distinct orange-red — and crawl into glazing overlaps, frame joints and the gaps under staging to overwinter. Clean in October and you sweep them out while they are static and concentrated. Clean in March and they have already woken up and dispersed across the whole structure.
The same logic applies to grey mould. Every dead leaf left on the floor is a spore factory, and the first thing those spores meet in spring is a tray of soft, crowded seedlings. And then there is light: between October and February there is so little of it that a film of green algae on the glass genuinely costs you growth. Anything you plan to overwinter under cover needs every photon it can get, which is one reason our guide to extending the growing season puts clean glazing near the top of the list.
Empty it first — and be ruthless
Everything comes out: pots, trays, canes, string, labels, half-bags of compost, and the plants themselves. You cannot clean around obstacles, and sorting is half the job.
Spent tomato, cucumber and pepper plants can be chopped and composted unless they showed blight or wilt, in which case bin them. Pull the roots out too. Old growbags are worth emptying onto an outdoor bed as a soil improver, but never reuse that compost for sowing — it is low on nutrients and high on whatever was living in it, which is a direct route to damping off. Anything genuinely spent goes on the compost heap or into a leaf mould bin. If you have green tomatoes still on the vine, pick them before you clear — our guide to ripening green tomatoes covers what to do with them.
The clean, step by step
- Dry-brush before you get anything wet Cobwebs, dead leaves and grit out of the corners and joints first. Wetting that debris turns it into a paste that takes three times as long to remove.
- Wash the glass, inside and out Hot water with a squirt of washing-up liquid and a soft brush. Work top down. The outside matters as much as the inside for winter light.
- Run a plant label down every glazing overlap This is the step that separates a proper clean from a wipe-over. A plastic label slid between overlapping panes drags out the black-green algae strip and the mites hibernating with it.
- Scrub the frame, the staging and the joints Aluminium channels and the undersides of shelves are where pests actually spend the winter — not on the glass. Get into every corner with the brush.
- Wash the floor and underneath the staging Gravel and slabs harbour slugs and spores. Lift and rinse loose slabs if you can; brush gravel through with hot soapy water.
- Rinse and dry with everything open Leave the door and all vents wide open on a breezy day until the structure is bone dry before you put anything back in.
Pots and trays: the step most people skip
A stack of reused module trays is the single most common cause of seedlings collapsing in spring. The residue in the cells carries fungal spores straight to the most vulnerable stage of a plant's life, and no amount of fresh compost on top makes up for it.
Wash every pot and tray you intend to reuse in hot soapy water with a brush, rinse, and dry them completely before stacking. If you had an outbreak of damping off, botrytis or any soil-borne disease this year, follow the wash with a garden disinfectant at the stated dilution. Terracotta needs a soak first — the white crust on the outside is mineral salts and comes off with a stiff brush. Store everything dry and off the floor, and it will be ready when you are sowing indoors in February.
Hot soapy water or disinfectant?
Hot soapy water and a brush
The right choice for a routine annual clean.
- Removes algae, grime, eggs and overwintering adults mechanically
- No dilution to get wrong, no residue, no waiting period
- Safe around plants you are bringing back in the same day
Garden disinfectant
Worth it after a bad year, not as a default.
- For a season with damping off, botrytis or a whitefly explosion
- Follow the dilution exactly and rinse any surface plants will sit on
- Apply on a mild day with doors open; keep it away from ponds and the compost heap
Whichever you use, the mechanical work does most of the heavy lifting. A disinfectant sprayed onto grime simply disinfects the grime. For persistent problems, pair the clean with the preventative measures in our guides to common plant diseases and common garden pests.
Setting up for winter: air, water and light
Once it is clean, resist the urge to seal it. Most winter losses under cover are fungal rather than frost damage, and stagnant damp air is what causes them. Open the vents and the door on mild days, even in December, and never leave wet foliage shut in overnight.
Drain and scrub the water butt while you are at it. Stored rainwater collects organic matter over a summer and carries the organisms responsible for damping off — fine for established plants, but use mains water for seed trays. Check the glazing clips, the door catch and the vent stays before the first autumn gale, because a pane that lifts in November will not be replaced until spring. If you plan to heat the greenhouse, bubble insulation is worth fitting now; if you do not, leave it off, since it costs light you cannot spare. A min–max thermometer is the cheapest useful thing you can hang in there.
What goes back in
A clean greenhouse in October is not an empty one. This is the moment to bring in chilli and pepper plants for their second year, set up herbs on the bench, and start trays of winter salad leaves and winter lettuce for picking from November. Modules of broad beans and sweet peas sown now and overwintered under cover will be weeks ahead next spring, and a windowsill tray of microgreens keeps something green going all winter.
One thing that should not go in: genuinely tender plants that need frost-free storage rather than light. Dahlias, pelargoniums and begonias want a dry shed or garage at 5–10 °C, as explained in our guide to overwintering tender plants. An unheated greenhouse gets colder than an unheated shed on a clear night. Meanwhile the genuinely hardy crops — leeks, parsnips, kale — stay outside where they belong.
Common mistakes
- Leaving it until spring. By March the overwintering pests have already woken up and spread.
- Cleaning the glass but not the frame. The glass looks worse; the joints are where the mites actually are.
- Reusing trays without washing them. The fastest route to damping off in a fortnight's time.
- Sealing it up for winter. Damp still air kills more overwintered plants than cold does.
- Putting bubble wrap on an unheated greenhouse. You trade light you need for warmth you will not get.
Frequently asked questions
When exactly should I clean the greenhouse?
As soon as the summer crops are finished — usually the last week of September through October, on a dry, breezy day so everything dries before nightfall. If you are still picking tomatoes, do the empty half now and the rest in a fortnight rather than waiting for one perfect day.
Do I really need a greenhouse disinfectant?
Not every year. Hot soapy water and a brush deals with a normal season. Reach for a proprietary disinfectant when you have had a specific problem — damping off, botrytis, a serious whitefly or red spider mite infestation — and follow the label dilution.
Should I put up bubble wrap insulation?
Only if you are heating the space and trying to cut the cost of it. Bubble insulation reduces light transmission noticeably, and in an unheated greenhouse over a British or Dutch winter, light is the limiting factor, not temperature.
Does this apply to a polytunnel?
Yes, with one adjustment: polythene scratches, so use a soft brush or cloth and no abrasive, and be careful with disinfectants that can degrade the film. The important parts — clearing debris, scrubbing the frame and hoops, washing pots and trays, and keeping air moving — are identical.
An afternoon in October buys you a clean start in February, which is the only time of year when a greenhouse really has to perform. While you are in the autumn tidying frame of mind, our autumn garden checklist covers the beds outside, and the seed storage guide deals with the packets you have left over. Then plan the year ahead with the sowing calendar, and browse lettuce, corn salad, spinach, herbs and microgreens — or everything at once in vegetables and the rest of our growing guides.
