when to transplant seedlings from seed tray

Seed Starting 101: Sowing & Transplanting Tips for Strong Seedlings

How do you turn that packet of tiny basil seeds into pots of lovely herbs for your garden? Starting plants from seed seems like a magical process, but there’s no great mystery to it. A few tips and pointers will help you on your way

You’ve set up light shelves and heat mats. You’ve sterilized your seed starting mix and considered other tips to prevent damping-off. You’ve ordered seeds for more plants than your yard and your neighbors’ yards together can possibly hold. You are more than ready to start turning your seeds into rows and pots of healthy seedlings!

Although it’s possible to sow seeds one by one into little pots on your light shelf, many plants seem to do better when transplanted once between sowing and being planted out in the garden. I usually start seeds in rows in shallow, domed seed starting trays. After the seedlings have their first true leaves (the first pair of leaves are cotyledons, or “nurse leaves”), they are potted up into individual pots or cell packs. For plants with a naturally branching or clumping habit such as basil or lobelia, I use a method that herb guru Tom DeBaggio calls “clump transplanting.”

You can purchase official “seed starting trays,” often with vented domes to hold a little extra humidity around the seedlings. Or you can create your own, using any container that will hold a good inch or so of potting mix. Take-out containers work great! Poke a bunch of holes in the bottom for drainage and in the top for ventilation. A hot metal skewer works well to make holes in a dozen nested containers at once. Separate containers after each jab so they don’t “weld” together. Be careful, and work in a well ventilated area.

Basil seedlings in closed vented container. Note little puff of condensation in lower left corner.

Use a good soil-less potting mix. If it’s not a “seed starting mix” as such, you may want to lighten it with a little extra perlite. I also add a pinch of polymer moisture crystals to my mix, so I don’t have to water as often. Fill your seed starting container with moist, preferably sterile mix. [1]

Petunia seedling tray, aka salad container. Droplets of condensation inside lid indicate too much moisture in potting mix.

Sow seeds in rows at least an inch apart, so that a row of well rooted little seedlings will be easy to break away. I sow seed quite thickly for clump transplanting. There’s generally no need to cover seeds; just press them gently into the surface of the potting mix. Don’t forget to label the container using a permanent marker or paint pen. Jot down the date also, to keep track of germination times.

When the container is closed, there should be enough humidity to make a little puff of mist on the inside of the lid. If large droplets of condensation form, then your mix is too wet — prop the lid open for a few hours to let it dry out a bit. The container can be easily watered from the bottom as needed. Place it in a tray of water for a few minutes, until it no longer feels lightweight.

At the first sign of germination, I make sure my seedling tray is as close as possible to the fluorescent light tube.[2] When seedlings have their first true leaves, and for sure by the time they have their second set of true leaves, they are ready to be transplanted. Looking at the seedling tray from the bottom, you can see vigorous roots searching for more growing room.

Tom DeBaggio’s clump transplanting method [3] makes for healthy, sturdy seedlings. It’s very simple. You don’t tease away a solitary seedling from the massed rootlets in the seedling tray. Instead, you gently separate a clump of seedlings and plant them together.

Having a larger clump of roots in the pot means it’s harder to drown the little seedlings. Damping off issues of root and stem rot are less likely when there are more roots to take up more water. With plants like basil, seedlings clumps give you a nice, full appearance before you even start pinching back the stems.

Tom recommends 3 or more plants in a clump. I’ve had young friends who enthusiastically potted up huge clumps of basil seedlings, and others who carefully selected a perfect pair. It’s all good. In Tom’s words, “I don’t count them, but take what comes apart most easily with the least root damage. It would defeat the beneficial effects. to prick out individual seedlings and gather them in clumps. the larger the leaves, the fewer seedlings [should be] in the clump.”

I like transplanting to pots no smaller than 48 cell inserts for standard nursery flats. Most of my seeds are started 6 to 8 weeks before planting out. Seedlings that will be started sooner (like wave petunias) or grow larger (like tomatoes) get a 2 inch pot. Fill pots or cell packs (“sheet pots”) with moist potting mix, and poke a hole in the mix with a stick or with your finger.

Handle seedlings by their leaves, and gently massage their roots to separate them into clumps. The tender stems should be touched as little as possible. Here’s Tom’s other piece of invaluable advice: “Set the seedlings into the pot lower than they were growing in the seedling flat,” preferably with the true leaves level with the growing medium and the cotyledons (nurse leaves) covered.

Gently pat the potting mix around the seedling clump. Water carefully around the seedlings to settle the potting mix around the roots. Your newly transplanted seedlings are ready to go back on the shelf, very close to the lights for best growth. After several more weeks, they will be ready for hardening off and planting out in your garden.

Sowing and transplanting is a straightforward, two-step process. There’s no “one true way” to go about it, but using covered seed starting trays and transplanting with Tom DeBaggio’s clump method definitely works for me. Before you know it, you will have turned a few seed packets into flats of beautiful seedlings for your garden!

Photos by Jill M Nicolaus

Move your mouse over the images for additional information.

[1] See my article “The Dreaded Damping Off (and How to Prevent It)” for tips on sterilizing seed starting mix.

[2] See my article “Seed Starting 101: Setting up Lights” for more information on the importance of light to growing sturdy seedlings.

[3] I owe a great debt to Tom DeBaggio and his “little book” that made me believe I could succeed in starting basil and other plants from seed. See my review in Garden Bookworm.

DeBaggio, Tom. Growing Herbs from Seed, Cutting & Root: An adventure in small miracles. Interweave Press, 2000. ISBN #: 1883010780

How do you turn that packet of tiny basil seeds into pots of lovely herbs for your garden? Starting plants from seed seems like a magical process, but there’s no great mystery to it. A few tips and…

Waiting to Transplant

Mark Macdonald | March 29, 2020

Many plants benefit from a head start by sowing indoors during late winter and early spring. For a few crops, notably peppers and tomatoes , this indoor start is an absolute requirement if growing from seed. These tender, tropical plants will be killed outright by frost, and will show immediate signs of distress if exposed to cold spring weather. So the gardener’s strategy is to make an educated guess about when it will be warm enough to transplant them outdoors, and work backwards from that date according to which crop is involved.

Tomatoes, peppers, and many perennial flowers require a good six to eight weeks of indoor growing before even considering peeking outside. But that’s a long time for plants to grow, so here are some strategies to consider while you are waiting to transplant outdoors.


Just about from the time the seeds are first placed into (or onto) the soil, bright overhead light is essential. With insufficiently strong light, seedlings will begin to grow tall and leggy from the very start. The seedlings are stretching their stem tissues, literally straining to get their leaves higher and closer to any light source so they can begin to photosynthesize and produce food for themselves. All seedlings do this, from tomatoes to palm trees.

If sufficient light is supplied, the seedlings have no need to strain and stretch, and they will remain stout and compact, with good colour and overall health. How does one provide sufficient light? Well, every grower has access to different tools. A heated greenhouse would be perfect for most seedlings, but these are expensive and few of us have access to them. So seedling lights are a smart option. Inexpensive T5 fluorescent tubes are available in several sizes. They produce full spectrum light in the frequency plants need for foliar growth. Even with a good double (or multiple) tube set up, it’s recommended that the tubes be kept 10cm (4″) above the tops of the seedlings. That may seem very bright, but one cannot over-apply light in this setting. The Growlight Garden is a self-watering kit with an adjustable hood that can be raised as the seedlings grow. And there lots of other ways to use the lights with adjustable stands . A superb, super-low energy alternative to T5 tubes is the recently developed LED light strips that fit most grow light fixtures.


Seedling Warmers do an amazing job of speeding up germination. They work with “bottom heat” which gently heats the soil above the ambient room temperature. This stimulates growth and really helps get plants started. But the gardener’s strategy is to keep the seedlings small and compact during this early indoor stage, so the mats should be removed or unplugged once germination occurs. Otherwise, they will continue to encourage fast growth, and the seedlings may become too large for their containers, or take up too much space indoors.

Even for heat-loving tomatoes and peppers, a warm growing space is not required during this nursery stage. Given ample light and a cool environment of around 18°C (64°F), the plants should grow slowly, but steadily, producing the healthiest transplants.

Air Movement

Seedlings will nearly always benefit from some movement of air indoors. This will help reduce excess moisture buildup and the possible mould and mildew problems that result from it. If their leaves and stems are subject to even slight movement, seedlings will develop stronger cell walls and be better prepared for the harsh elements of the great outdoors. If seedlings were started under domes, it’s a good idea to remove the domes after germination so that air can move freely and excess moisture can evaporate from the soil and trays. A very basic table fan is all that is needed to improve air movement for the benefit of seedlings.


There are numerous reasons for encouraging compact growth while waiting to transplant seedlings outdoors. As seedlings grow, they begin to compete with their neighbours for light, and if they are planted together, for nutrients and moisture. The gardener’s strategy here is to prevent unnecessary competition between seedlings. So lots of light and a cool environment will help. But plants continue to grow beneath the soil just as quickly as they do above.

This is a good reason to not fertilize seedlings prior to transplant. Fertilizer produces strong, fast growth, which is not wanted at this early stage. Seeds contain enough food to produce the initial cotyledon or first pair of leaves. These are then used by the plants to produce their own food, through photosynthesis, to allow for the growth of new tissues. Until they need to really go to work at transplant time (and after), the plants need no further nutritional help.

Potting On

The phrase “potting on” describes the gradual transition from seedling tray to small pot, and from small pot to slightly larger pot, as needed, as the seedlings grow. If cold weather persists outdoors, transplanting may be delayed by weeks. And even with the light, space, and environment described above, most seedlings will eventually out-grow their root space.

Most plants are not bothered by potting on, but it should be done with great care not to damage the delicate root system, and without bruising the leaves and stem. Handling seedlings by the root ball is often safest. Refer to specific instructions about each type of plant in question.

Some plants respond very poorly to transplanting, so if they absolutely must be started indoors, it’s a good strategy to use peat , coir , or newspaper pots , or Cow Pots , that can be transplanted, pot and all, into a larger container, or into the garden row. This prevents the seedling from having its roots disturbed, and they will eventually penetrate the pot as it biodegrades in the soil. Soil Blockers are a fantastic alternative for small farms or nurseries, or wherever large numbers of seedlings need to wait for transplanting.

When to Transplant?

The question of when to transplant seedlings is absolutely tied to regionality. The last average frost date in a given region is a very general tool for estimating how many weeks later is appropriate for transplanting. A basic plan can be used by employing our Regional Planting Charts , but it takes careful management to get this right. For peppers, tomatoes, and most tender seedlings, a good rule of thumb is to wait until night time temperatures are steadily at (or above) 10°C 50°F before even contemplating transplants outdoors. It may work earlier with the help of a greenhouse, cloche cover, or cold frame, but that’s another subject.

All seedlings will benefit from hardening off – the process of gently acclimatizing to direct sunlight, cool temperatures, wind, and night/day temperature fluctuations. These can all cause transplant stress, so hardening off is a key step to success.


I like to think of the indoor seedling stage as an artificial holding area. We want the seedlings to be at their peak possible health once we transplant them. Before that, though, they’re still young. They’re still in school. Only when they actually get transplanted do we put them to work. It’s that key point when they’ll benefit from organic fertilizer to give them the push into the proper growing season. After transplanting is the real time to help these plants accomplish their goal, to mature, and to produce the leaves and fruits that make all this work worth while.

Learn some expert gardening advice on when to transplant seedlings, along with some key organic gardening strategies for producing the healthiest seedlings.