Starting Seeds in Foam Cubes for Hydroponics: Step by Step

Starting seeds without soil

Foam cubes: how I start every plant

Preparing the mat, setting the seeds correctly, keeping them moist, thinning and transplanting: the steps that make every sowing work for me. You will find germination temperatures and germination times of all plants on my page Germination temperatures and times.

🧽

1/3 in water

the mat soaks itself from below

🌱

1 seed per cube

herbs as a bunch of 3 to 6

🌗

light or lid

light germinators open, dark germinators under the lid

🚫

no fertiliser yet

only once the seed leaves are open

Why I start seeds in foam cubes

There are many options for starting seeds: rock wool, starter plugs, coco or foam. I prefer foam cubes. They are cheap, clean and pH neutral, they do not crumble, and nothing dissolves that later floats around in the system. The roots simply grow through.

The biggest advantage comes when transplanting: the cube simply moves into the net pot with the plant. Nothing has to be rinsed off, and the fine roots stay undamaged. That is why the cube is my favourite method as soon as there are many plants. Every year I start around 36 tomatoes of different varieties, and that easily fits in two propagation boxes.

Material	What I say about it
Foam cubes	my choice: clean, pH neutral, does not crumble
Rockwool	common in commercial growing, untreated it can raise the pH
Seed plugs	good alternative, can crumble a little in the system
Coco	fine for a few plants, must be rinsed before moving

1Preparing the mat

once before the first use

The foam mat comes from the factory. That is why I first wash it hot so that no residues from production remain. Then I rinse it cold so that the seeds do not go into a hot mat.

In the propagation box I put a grid, such as a draining rack, and the mat on top. Underneath, the roots will have room later. The mat stays in one piece, because the connected cubes keep each other moist. Then I pour in enough water that about a third of the mat stands in water. It soaks itself from below without the seeds lying in water.

Washing

hot, then cold

Base

grid

Water level

mat 1/3

Nutrient

none yet

I use my seedling box with lid and 25 cubes and for many plants the Foam mat with 100 cubes.

2Setting the seeds

how many, and how deep

How many seeds go into one cube depends on what you want to harvest later. Plants that grow individually get one seed from me. With many herbs, on the other hand, I want a small bunch, so depending on the plant 3 to 6 seeds go into one cube.

One seed per cube	Several seeds for a bunch
Lettuce, pak choi, kohlrabi	Parsley, chives
Tomato, pepper, chilli	Dill, coriander
Cucumber, basil	Rocket

If your seeds are older or weak, it is better to set 2 seeds per cube. A germination test shows you whether they still germinate well: 10 seeds on damp kitchen paper, cover, put somewhere warm and count after a few days. If 8 out of 10 germinate, your seeds have a germination rate of 80 percent.

Light germinators: press lightly, leave uncovered

Light germinators such as lettuce, basil or rocket need light to germinate. I put the seed into the slit of the cube and only press it lightly. Nothing is covered. If a light germinator sits too deep, it gets no light and germinates poorly.

Dark germinators: do not press in, lid on

Dark germinators such as tomato, pepper or parsley germinate better in the dark. You do not have to press them in. I put the seed into the slit the same way and simply put the lid on the propagation box. Underneath it is dark, and the moisture stays in. Check dark germinators every day: as soon as they have germinated, the lid comes off and they need light immediately.

Light and dark germinators in one box?

The easiest way is to start them separately: light germinators uncovered under the lamp, dark germinators in a box with a lid. Which plant is which germination type and which temperature it likes is in my table under Germination temperatures and times.

Peppers germinating in a foam cube in hydroponics — Pepper is a dark germinator: it germinates under the lid and then goes straight into the light.

3Keep moist and warm

the first days

The surface of the cubes dries out quickly. That is why I spray the seeds from above every day. It is even easier with cling film or a zip bag over the box. Then the moisture stays in, nothing dries out and you do not have to spray. Light comes through the film, which suits light germinators. For dark germinators you use the lightproof lid.

Every plant has its comfort temperature. Lettuce likes it cool; above 24 °C it germinates worse. Tomatoes, peppers and chillies, on the other hand, need warmth; below 20 °C they germinate only slowly. You keep the warmth most precisely with a heat mat with thermostat. I put the sensor into the water of the box, where it measures the temperature right at the cube. The fan stays off during germination, otherwise the cubes dry out.

My chamomile bath for valuable seeds

Seeds that are important to me or of which I only have a few I soak before sowing: tomatoes, peppers, chillies and older seeds. For this I brew a bag of chamomile tea, let it cool to lukewarm and soak the seeds in it for 12 to 24 hours. Then I sow immediately and do not let them dry again. The seed soaks itself full beforehand and germinates faster. Chamomile contains substances that inhibit fungi. Whether the bath really protects the seeds is not scientifically proven, but I have had very good experiences with it. I do not soak very small seeds.

Spider Farmer heat mat with thermostat

For seeds that like it warm, such as tomato, pepper and chilli. You put the sensor into the water of the propagation box.

* Affiliate-Link: Bei einem Kauf erhalte ich eine Provision, dein Preis bleibt gleich. Preis inkl. MwSt., zzgl. Versand, Stand 8.11.2026. Bilder: Amazon Creators API

Angebot

Gloria hand sprayer

I use it to spray the seeds in the propagation box from above every day.

* Affiliate-Link: Bei einem Kauf erhalte ich eine Provision, dein Preis bleibt gleich. Preis inkl. MwSt., zzgl. Versand, Stand 8.11.2026. Bilder: Amazon Creators API

* Affiliate links (Amazon): if you buy, I receive a commission; your price stays the same.

4Germinated: lid off, light on

now comes the first fertiliser

As soon as the seeds have germinated, film and lid come off. If the film stays on longer, mould quickly forms in the humid air. By the way, white fuzz directly on the root is not mould; those are root hairs. And a green film on the cube is algae. It grows where it is moist and bright, and it is harmless.

Germinated means: straight into the light. If seedlings get too little light, they stretch and become long and thin. With the propagation box the lamp hangs from above, about 20 to 30 cm above the plants, and shines 14 to 16 hours a day, never longer.

During germination there is only water, because the seed has its own nutrient reserve. Once the seed leaves are open, I give 0.5 ml of my liquid fertiliser per 1 litre of water. From a plant size of 2 to 3 cm I use 1 ml. These amounts only apply to my fertiliser. With a different fertiliser, follow its instructions and dose by EC value.

Light

14 to 16 hrs

Lamp

20 to 30 cm

seed leaves open

0.5 ml / l

from 2 to 3 cm

1 ml / l

Starting seeds creates a lot of moisture in the air. That is why I open the window wide for about 15 minutes every morning. You can read more about this in the post Humidity and air circulation.

From my shop

Everything for your soil-free start

HydroFlex Tower for indoors and outdoors, seedling box, seedling station, support rings and my own nutrient. After you buy, I’ll help you on WhatsApp.

To the shop ›

5Thinning

when two germinate in the same cube

If two plants have germinated in a cube where one should be enough, the stronger one stays. I cut off the weaker one with small scissors directly above the cube instead of pulling it out. That way the roots of the other plant stay undamaged. With herbs for a bunch, of course, all of them stay.

6Transplanting into the propagation station

from about 2 cm with first roots

I transplant when the seedlings are about 2 cm tall and the first roots are growing out of the bottom of the cube. That is easy to check: lift the cube and look underneath. No roots yet? Then give them a few days. Anything that has not germinated yet may keep germinating in the box.

I take the cube with the plant out of the mat and put it into a net pot of the propagation station. Hold the cube, not the plant, and do not bend the roots. At first the pot dips at most 0.5 cm into the water. Only when 2 to 3 cm of roots stick out at the bottom of all plants do you lower the water level so that about 1 cm of air remains. The air bubbler runs there from the start, day and night.

My propagation stations are available for 13, 25 and 35 plants, for example the station for 25 plants and the station for 35 plants. How things continue with lettuce afterwards, you can read in the post Growing lettuce without soil.

Why I do not germinate directly in the tower

My first attempt was exactly that: seed in the cube, cube in the tower. Many seeds did not germinate, and what came up got long, thin stems. In the tower the cube sits several centimetres deep in the net pot, so in a dark hole. On top of that, the tower already needs a pump, light and power for starting seeds. In the propagation box a small lamp is enough.

If it does not work: the most common mistakes

What you see	Usually the cause is	What helps
Seed rots	cube stands too deep in water	mat only a third in water
Seed dries out	surface dries out	spray daily or cover with film
Light germinator does not germinate	too deep in the cube	only press lightly, leave uncovered
Dark germinator germinates poorly	too bright	lid on the box
Lettuce does not germinate	too warm	cool spot, not on the heater
Tomato, pepper germinate slowly	too cold	heat mat with thermostat
Mould on the cubes	film or lid left on too long	remove immediately after germination
long, thin seedlings	too little light	lamp right after germination
nothing germinates at all	old seeds	do a germination test, new seeds

Do not give up too early. Some herbs take two to three weeks, and not every seed is equally fast. How long each plant takes for me is under Germination temperatures and times.

Frequently asked questions about starting seeds in foam cubes

Why do I use foam cubes for starting seeds?

They are cheap, clean, pH neutral and do not crumble. Nothing dissolves that later floats in the system, and the roots simply grow through.

Do I have to rinse off soil when the plant comes out of the cube?

No. The cube simply goes into the net pot with it. You only have to rinse plants from soil or coco.

What is the difference between foam cubes and rock wool?

Rock wool is often used in commercial growing. Untreated rock wool can raise the pH value. I use foam cubes because they are pH neutral and work reliably for me.

Do I have to wash a new foam mat before the first use?

Yes. First wash it hot to remove residues from production. Then rinse it cold so that the seeds do not go into a hot mat.

How much water goes into the propagation box?

Enough that about a third of the mat stands in water. It soaks itself from below without the seeds lying in water.

Why does the mat stay in one piece?

The connected cubes keep each other moist. Individually they dry out faster.

What is the grid under the mat for?

A grid, such as a draining rack, raises the mat a little. Underneath, the roots have room.

How many seeds go into one cube?

Plants that later grow individually, such as lettuce, pak choi, kohlrabi, tomato, pepper, chilli, cucumber and basil, get one seed. Herbs that should grow as a bunch, such as parsley, chives, dill, coriander and rocket, get 3 to 6 seeds depending on the plant.

When do I put two seeds in one cube?

When your seeds are weak. If less than half germinate in the germination test, it is better to set 2 seeds per cube or buy new seeds.

How do I set light germinators in the cube?

Put light germinators such as lettuce, basil or rocket into the slit and only press them lightly. Nothing is covered; they need light to germinate.

How do I set dark germinators in the cube?

Put dark germinators such as tomato, pepper or parsley into the slit the same way. You do not have to press them in. You simply put the lid on the propagation box; underneath it is dark.

What happens if a light germinator sits too deep in the cube?

Then it gets no light and germinates poorly or not at all. That is why you only press light germinators lightly.

How do I keep the cubes moist during germination?

Spray the seeds from above every day or put cling film or a zip bag over the box. For dark germinators you use the lightproof lid.

When do film and lid come off?

As soon as the seeds have germinated. If the film stays on longer, mould quickly forms in the humid air. Check dark germinators every day.

Is the white fuzz on the germ root mould?

No. White fuzz directly on the root is root hairs. Mould tends to form when film or lid stay on too long after germination.

Is a green film on the cube bad?

No. Where it is moist and bright, algae grow. That is harmless and only shows that light and wetness come together.

Why are my seeds not germinating in the cube?

The most common causes are the wrong temperature, a cube that is too wet or dried out, light germinators set too deep and old seeds.

What happens if the cube stands too deep in water?

Then the seed gets no air and rots. That is why the mat only stands a third in water, and the surface only stays moist.

What is the chamomile bath for seeds?

I soak valuable seeds such as tomato, pepper, chilli and older seeds in lukewarm chamomile tea for 12 to 24 hours before sowing. Then I sow immediately. I do not soak very small seeds.

Does the chamomile bath reliably protect the seeds from fungi?

That is not scientifically proven. Chamomile contains substances that inhibit fungi, and I have had very good experiences with it. What is certain: the seed soaks itself full beforehand and germinates faster.

When do the seedlings get fertiliser?

During germination there is only water. Once the seed leaves are open, I give 0.5 ml of my liquid fertiliser per 1 litre, from a plant size of 2 to 3 cm 1 ml. These amounts only apply to my fertiliser.

What do I do if two plants germinate in one cube?

The stronger one stays. Cut off the weaker one with small scissors directly above the cube instead of pulling it out. That way the roots of the other stay undamaged.

When do I move the cube into the propagation station?

When the seedlings are about 2 cm tall and the first roots grow out of the bottom of the cube. Lift the cube and look underneath.

How deep does the pot stand in water after transplanting?

At first at most 0.5 cm. Only when 2 to 3 cm of roots stick out at the bottom of all plants do you lower the water level so that about 1 cm of air remains.

Why do I not germinate directly in the tower?

In the tower the cube sits deep in the net pot, so in the dark. Light germinators get too little light there, and the tower already needs a pump, light and power for starting seeds. In the propagation box a small lamp is enough.

Why do I start cucumbers directly in the foam cube?

Cucumbers have sensitive roots. They should not later have to be freed from soil and washed out first.

You will find all germination temperatures and germination times under Germination temperatures and times. Next up is growing media, the Net pot and lighting.

Continue with your own growing

My book

Step by step into hydroponics

168 pages, simply explained for beginners and with videos on the topics (in German). Exactly how I grow myself: from sowing to harvest.

More about the book ›

Free

Which tower suits you?

A few questions about space, location and what you want to harvest, and you get a recommendation.

To the tower advisor ›

Questions about your setup? Message me on WhatsApp.

Tapping opens WhatsApp (provider: WhatsApp Ireland Ltd.). More in the privacy policy.