How to Save Time Growing Microgreens: A Step-by-Step Guide

August 30, 2026

Image credit: Image by nattanan23 from Pixabay

Most advice on growing microgreens focuses on price: cheapest seed, cheapest tray, cheapest light. But price was never really the question we should have been asking.

Over several articles in our Microgreen Tray Guide, we actually timed our own workflow, stage by stage, comparing generic trays against the Bootstrap Farmer system we've grown on for years. None of the individual differences looked dramatic on their own. A few seconds here, a minute there. But microgreens are a repetition business. You don't fill one tray a week, you fill dozens, sometimes hundreds. Small friction, repeated that often, turns into hours.

This guide walks through the whole growing cycle, from choosing a tray system through to harvest and turnover. Some of it comes from those timed tray tests, and some of it is just what's worked for us in the equipment and layout around the trays themselves.

Step 1: Choosing Your Tray System

Every downstream step gets easier or harder depending on the tray decision you make before you've even sown a seed.

Size. Most growers standardise around the 1020 tray because it fits standard shelving and microgreen racks, and consistent sizing makes stacking, watering and harvesting more predictable.

Depth. Microgreens are harvested young, usually within one to three weeks, so their root systems stay shallow. Deeper trays mean either more soil to buy, store, carry and clean up, for no real benefit to most crops or only partially filling the tray. This can cause stagnant air around your microgreens when growing and make it hard to harvest. We went deep on this in How Deep Should Microgreen Trays Be?, and the short version is: unless you're growing a lot of sunflower shoots or similar, shallow trays are the better default. Even then, sunflowers grow just fine in shallow trays.

Durability. A tray that cracks, warps or sticks stops being a tray and starts being a daily annoyance. We compared wall thickness and plastic grade in The Strongest 1020 Microgreen Trays in New Zealand; heavy-duty trays hold their shape through full sun and summer heat, black included, where thinner trays warp and buckle after a few rounds of drying outside.

Get this step right and every stage below gets a little easier. Get it wrong and you're compensating for it every single day. If you'd like to see the trays we use, browse our Bootstrap Farmer 1020 shallow trays or the full Bootstrap Farmer range.

Step 2: Filling Trays with Growing Medium

This is where we ran our first real stopwatch test. We filled five trays of each type with the same soil, the same person, the same process.

Bootstrap Farmer trays: two minutes for five trays.
Generic trays: three minutes for five trays.

One extra minute per five trays doesn't sound like much, until you're filling dozens of trays a week. The cause is usually wiping rims that catch soil while you fill, separating trays that are sticking together, or having to find matching holes with no holes trays in a stack of black trays. Full detail (and the maths behind it) is in Are Heavy-Duty Microgreen Trays Worth It? We Timed the Difference.

Step 3: Sowing and Sterilising

Once trays are filled and seed is sown, we water them in and go over the surface with a peroxide spray to sterilise before the tray goes into germination. This one has nothing to do with which tray you use, but it's one of the easiest time-savers in the whole process if your equipment is right.

We use an 8-litre pump-up pressure sprayer with a long hose and a teat sprayer trigger, the same style dairy farms use in a dairy shed, sourced from a local dairy supplies company. It's solid, well-built, and has held up to years of daily use. The real time-saver, though, is where it lives: we hang it from the ceiling on a pigtail-style hose right above where we sow, so it's always there ready to grab rather than stored somewhere and fetched each time we need it. It also saves time constantly refilling and pumping a hand held pump up sprayer.

It sounds like a small thing, but the time saved having it hanging exactly where you need it adds up.

Step 4: Stacking for Germination

Germination isn't really a stage you can put a stopwatch to, but rim quality still shows up here in a smaller, practical way.

Some seeds are small enough that they don't like any weight sitting on top of them while they germinate. For those, we use an upturned solid tray as a blackout dome that simply holds moisture in, with no weight involved at all. This is where rim width matters: Bootstrap Farmer's wider rim means the domes sit on each other properly, where the narrower, rounded rims on cheaper trays let them slide straight off. This gets really tricky and precarious when you need to stack several more trays on top, each with their own dome. It becomes a bit of a stack of cards unless your using solid trays with a flat rim.

It's a small thing, but a dome that won't sit still in a cupboard is one more fiddly job at the end of a long day.

Step 5: Watering

We bottom water using a trigger nozzle to control the flow, lifting the top tray slightly with one hand while triggering water with the other. When trays separate cleanly, that's easy to manage one-handed. When they stick, you're suddenly fighting trays apart with both hands while also trying to hold the trigger, which is a lot harder to do cleanly.

Like our sterilising sprayer, the watering trigger hangs from the ceiling on a pigtail hose, one at each end of the workspace, so it's never dragging across the floor. It's always right there to grab for topping up trays, filling bottles, or a dozen other quick jobs, rather than something you have to walk off and find.

We timed watering four trays at a time:

Bootstrap Farmer trays: 19 seconds for four trays.
Generic trays: 28 seconds for four trays.

Scaled up to our farm, watering around 100 trays a week at roughly four waterings per growing cycle, that nine-second difference works out to about 15 minutes saved every week, or roughly 13 hours a year, from watering alone. Full workings are in Do Microgreen Trays Affect Watering Time?

Step 6: Harvesting

This is where tray depth comes back around to matter again. In a deep tray, the crop sits well below the rim, which forces an awkward cutting angle. That's slower, and it tends to leave sellable yield behind on the root mat because you can't get the blade in cleanly. In a shallow tray, the crop sits close to the rim, so you can cut straight across in one clean pass.

If harvesting feels slower or messier than it should, it's worth checking whether tray depth, not your technique, is the actual problem.

Step 7: Washing, Sorting and Turnover

Between harvests, every tray gets washed, sorted and stacked ready to go again, and this is where we found our single biggest time saving, plus the biggest durability difference.

Washing itself isn't the hot-dishwasher, commercial-steriliser process people sometimes picture, a full cycle like that can't handle the volume anyway. Most growers wash cold, in a sink with a scrubber. We use a tray washing system with a water blaster, which speeds this step up considerably.

The real durability test comes after washing, when trays dry in the sun. Cheaper trays warp and buckle in summer heat, especially dark colours that pull in more heat from the sun. Heavy-duty trays hold their shape through that heat, black included, which is usually the real reason a cheaper tray stops sitting flat long before it actually cracks.

We use black bottom trays (no holes) paired with coloured top trays (with holes), one colour per variety per sowing day. Before we set this up, sorting trays after washing could take up to half an hour every week, and mistakes still slipped through: a no-holes tray on top starves a crop of water, a holes tray on the bottom floods your shelf. With colour-coding, trays match up like a "licorice stack", holes and no-holes alternating correctly, and sorting stops requiring any thought at all. That's covered in full in Are Heavy-Duty Microgreen Trays Worth It? We Timed the Difference.

Holding shape through repeated sun-drying is what keeps trays in rotation for years instead of needing constant replacement, meaning fewer mid-season gaps in your tray count and less time spent culling warped trays from the stack.

Step 8: Laying Out Your Station

The last time-saver isn't a piece of equipment at all, it's the shape of your workspace.

Soil, filling and sowing, and wherever finished trays get emptied at the end, should sit in a logical line, so you're moving forward through the process rather than criss-crossing the room. Every extra step you take between stations is a small tax paid on every single tray, and across a real harvest day, that adds up to more lost time than any one piece of gear.

If you're not sure where to start, watch yourself, or someone else, work a tray from empty to finished, and count the steps that weren't strictly necessary. Rearranging a bench or moving one station a metre closer to another costs nothing, and it's often the biggest single change you can make.

Adding It Up

None of these numbers look dramatic in isolation. A minute here, fifteen seconds there, half an hour a week on sorting. But run the maths across a real farm and it changes shape fast.

In How Much Do Your Microgreen Trays Really Cost? we modelled a small commercial operation running about 100 flats a week, roughly 500 trays in rotation, and took a conservative view: just 8 minutes of extra friction per day from filling, sorting and fixing mistakes on lower-quality trays. At $30 an hour, that's about $1,456 a year in extra labour, before you even count tray replacement costs from trays that crack or warp every couple of years instead of lasting a decade.

Add the roughly 13 hours a year from watering alone, and the picture is clear: the sticker price of a tray was never really the cost that mattered. The daily friction was.

Frequently Asked Questions

Does tray choice really make that much difference to how long harvest day takes?

On its own, one stage might only save you a minute or two. But growing microgreens means repeating filling, watering, harvesting and washing on the same trays week after week, so small per-tray savings compound into real hours over a year.

What's the single easiest change to make first?

Colour-coding your tops and bottoms tends to give the fastest payback for the least effort. It's a one-off setup that removes an ongoing weekly sorting job almost entirely.

Do I need heavy-duty trays if I'm only growing for my own family?

The time savings scale with volume, so they matter less at hobby scale. But durability still counts: a tray that lasts a decade instead of a season is still less hassle even at low volume.

Do I need to sterilise seed before it goes into germination?

A peroxide spray straight after watering and sowing is a simple, effective sterilising step before trays go dark to germinate. Whether you'll actually do it every time usually comes down to how handy your sprayer is; keeping ours hanging right where we sow means it never gets skipped.

Do stacked trays need to be weighted down during germination?

Generally yes for most microgreen crops. Adding a weighted tray on top holds the seed down as it germinates, helping it push its root into the soil. A dome's main job is holding moisture in, not applying pressure, and small-seeded crops like basil and amaranth in particular don't want weight sitting on top of them while they germinate.

What's the quickest way to speed up watering?

Bottom-watering with a trigger nozzle you can operate one-handed, paired with trays that separate easily, makes the biggest difference. Hanging the hose itself off the floor and within reach, rather than dragging it across the room each time, saves more time than it sounds like it should.

Is workspace layout really as important as equipment?

Often more so. A bench arranged so soil, filling, sowing and emptying flow in one direction removes unnecessary steps from every single tray, and across a full harvest day that adds up to more than any one piece of equipment will save you.

More from the Microgreen Tray Guide

This guide draws on the full series, where we go deeper on each stage:

Ready to build your own setup? Browse our 1020 shallow trays, LED grow lights and reusable silicone mats.

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