You’ve planted tiny seeds and now they’re rapidly taking off. Under your grow lights is a sea of green leaves.
You can hardly even see the seed starting trays beneath anymore.
So, now what?
The moment your seedlings outgrow their starter cells is exciting. It’s living proof you’ve been doing a fantastic job so far.
But it’s also a crucial time.
They’re running out of room in their tiny cells and need to either be planted out or potted up into larger containers.
If the weather is cooperating, you can gently harden them off and transition them to a happy life out in the garden.
But if it’s still weeks before your last frost date, you’ve got to transplant seedlings to bigger pots so they can keep growing strong.
This post will cover the signs your seedlings need a bigger pot, when and how to pot up seedlings, and how to prick out and separate seedlings — so you can do it all without losing plants along the way.
Need help getting to this point? Read my complete guide to indoor seed starting first, then come back when your seedlings are ready to be potted up.
Pricking Out Seedlings
First, let’s talk about pricking out seedlings.
Pricking out is the process of gently removing small seedlings that were sown closely together in a large container and transplanting them into their own individual pots.
Why Sow Seeds in a Single Flat
Some seeds are best started when sown densely in a single flat or tray rather than individual cells.
You might do this with older seeds you’re not sure will germinate, very tiny seeds that are difficult to space in individual cells, or slow-germinating seeds that benefit from a covered tray that stays consistently moist.
Once those seedlings have sprouted and grown their first true leaves, that’s when you would prick them out into individual pots.
True Leaves vs. Cotyledons
What’s the difference between true leaves and cotyledons?
Cotyledons are the very first leaves that appear when a seed sprouts. They may be rounded or narrow and don’t look much like the mature plant at all.
True leaves are the second set of leaves, and they look like a miniature version of the plant’s adult leaves.
Wait for the first true leaves to appear before pricking out. You want seedlings large enough to handle, but not so large that they’re difficult to separate from their siblings.
How to Prick Out Seedlings
Step 1
Water the seedling container thoroughly before you begin.
Moist soil releases seedlings much more easily than dry soil, and you’ll do a lot less root damage. While the water soaks in, prepare the transplant pots. Fill them with moist potting mix and make a small hole in the center of each.
Step 2
Grab a chopstick, pencil, or dibber to prick out seedlings.
Working from the edges of the container toward the center, insert your tool at an angle slightly away from the seedling you’re targeting, going down about twice the height of the seedling.
Slowly lever the tool upward to scoop the seedling up and loosen it from the soil.
Here I’m working with multiple seedlings in small cells, but if you had a large flat, it’s best to start with seedlings that have a bit more space around them. They’re easier to free without disturbing their neighbors.
Step 3
Once it’s loose, hold a leaf and gently lift the seedling free.
Always handle young seedlings by the leaves.
If a leaf breaks, plants can recover, but a pinched or broken stem is usually fatal.
Step 4
Lower the seedling into the hole in the new pot, using your dibber to guide the roots into place if needed.
Tuck soil gently but firmly around the seedling and water it in. Then move on to the next one until all your pots are filled.
How to Separate Crowded Seedlings
If you planted two or three seeds per cell (as typically recommended), you may find yourself with multiple seedlings sharing one small pot.
Don’t toss the extras! Separate them and repot to get more seedlings.
This works best for plants that don’t mind a little root disturbance: tomatoes, peppers, eggplant, sage, basil, cabbage, broccoli, kale, onions, celery, gomphrena, amaranth, marigold, and snapdragons… These all tend to bounce back well for me.
Most of the plants you’d be starting indoors can be separated and repotted.
More delicate plants like zinnias, cucumbers, sunflowers, and squash are better thinned by snipping than separated.
These plants are better off being direct-sown anyhow. Here’s a guide to sowing zinnia seeds if you need it, and also how to grow cucumbers from seed.
To separate multiple seedlings growing in one cell:
- Water the pot well and let it soak in for a few minutes.
- Gently squeeze the pot and pop the whole root ball out.
- Hold half the root ball in each hand and pull apart slowly and steadily, not with a quick jerk, but with gradual, even pressure.
- Transplant immediately. Don’t leave bare roots sitting out.
Tips
If you have three seedlings, separate one from the clump first, then separate the remaining two.
If the roots are so tangled you can’t separate them without tearing, don’t force it. Snip the weakest seedlings off at soil level with scissors rather than risk damaging the roots of the one you want to keep.
How to Decide Which Seedling to Keep
As you’re pricking out or separating seedlings from a cell, you’ll often wind up with more seedlings than pots. So how do you choose which ones earn a spot?
The best seedling isn’t necessarily the biggest or the tallest. Instead, look for:
- A thick, sturdy stem; this is your best indicator of a healthy, vigorous plant
- Large, well-formed true leaves with good coloration
- A visible, well-developed root system when you tip it from the pot
When in doubt, choose short and stocky over tall and leggy every time.
Signs Your Seedling Needs a Bigger Pot
Knowing when to repot seedlings is half the battle. Here are the signs to watch for:
1. Roots coming out the bottom. Lift the pot and peek underneath. If roots are circling the drainage holes or poking out, your seedling has officially outgrown its home and needs a bigger pot as soon as possible.
The photo below shows seedlings at the ideal stage for up-potting.
2. Growth has stalled. You may have marveled at how fast things were growing, and now it seems like your seedlings have hit pause even with good light, consistent watering, and regular fertilizing.
A root-bound plant has nowhere left to grow, and it shows above the soil.
3. Yellowing or browning lower leaves. Yellowing can signal a lot of things, but if you’re doing everything else right, it may mean the plant needs more room to access nutrients.
4. Soil dries out too fast. If you’re watering daily or even twice a day and the soil still dries out within hours, that’s a sign that roots have taken over so much of the pot that there’s barely any soil left to hold moisture.
5. Plants look crowded or top-heavy. If the plant is more than twice the height of its pot, or it keeps tipping over, it’s time.
6. Five or more weeks since germination. Even if your seedlings look okay, if they’ve been in the same pot for five or more weeks without being potted up, go ahead and move them. Plants can become root-bound before the visible signs appear.
When NOT to Pot Up
Here’s a tip that will save you time and stress: if your plants are looking reasonably healthy and you’re less than two weeks away from outdoor transplant time, don’t bother potting up. Just wait.
There’s no point stressing your plants with another move if they’re going in the ground soon anyway. Hold off, harden them off, and plant them out.
How to Choose the Right Pot Size
Think of potting up like buying your kid the next size up in clothes. You wouldn’t grab something three sizes too big, they’d be swimming in those clothes. Instead, you’d choose the next size up. Same logic applies to seedlings.
Choose a pot that’s just one size larger than what they’re currently growing in. Going too large leaves excess soil that holds moisture your seedling’s roots can’t reach yet, which can lead to root rot.
A practical way to check: if you set the old pot inside the new pot, there should be just enough room to fit a finger all the way around the outside. That’s the right fit.
A common progression to follow:
- typical 6-cell starter pack → 2.5″ to 3″ (6–8 cm) pot
- 2.5″–3″ pot → 5″–6″ (13–15 cm) pot
- generally, choose a pot 1–2″ (3–5 cm) larger than the previous one
And always, always, always choose a pot with drainage holes. If the container you’re using doesn’t have any, just drill or punch some in the bottom before planting up.
Looking for pot ideas at different price points? Check out my post on seed starting pots.
How to Pot Up Seedlings Step by Step
Step 1
Water the seedling well before beginning to pot it up.
Moist soil holds together better, making the root ball much easier to remove in one piece. It also reduces transplant shock.
Step 2
Prepare the new pot with fresh, moist potting mix. Don’t use seed starting mix at this stage. That’s for germination, not growth, and it doesn’t contain the nutrients your seedlings now need.
Fill the new pot most of the way and make a hole roughly the size of the root ball.
Step 3
Remove the seedling from its old pot carefully.
Squeeze the sides of a flexible pot to loosen the soil. Then place your hand over the top of the pot with the seedling stem between your fingers, flip it upside down, and give the bottom a firm tap to release it.
For pots with large drainage holes, you can also gently push up through the hole with a finger to pop the root ball free. Whatever you do, hold the seedling by its root ball or by a leaf, never by the stem.
Step 4
Set the seedling into the new pot. Keep it at the same depth it was growing before.
The one exception is tomatoes: you can bury them deeper, right up to the lowest set of leaves. Tomatoes grow roots all along their buried stems (called adventitious roots), so deeper planting actually makes them stronger.
Learn all my tips and tricks to growing the best-tasting tomatoes from seed in this post.
Step 5
Firm soil gently around the root ball and water in well. You want good contact between the roots and the new soil, without compacting it so tightly that drainage suffers.
Step 6
Get them back under the grow lights as soon as you’re finished so they can continue to grow.
After Potting Up: The Next 48 Hours
Don’t be alarmed if your seedlings look a little droopy or sad right after potting up. Some wilting is completely normal as they adjust to the move and re-establish their roots in the new soil.
What’s not normal: stems collapsing, leaf drop, or soil staying soggy for days.
Keep an eye on newly potted seedlings for the first day or two to make sure they’ve settled into their new homes. Let them have a break from the fan and don’t water them again until their pots have dried out on top.
Hold off on fertilizing for 2-3 weeks. New potting soil should already have some fertilizer mixed in, so adding more is not necessary.
After a couple of days, most seedlings will have perked back up and resumed growing. Continue your normal care routine from there.
Common Mistakes When Potting Up Seedlings
Going too many pot sizes at once.
It’s tempting to pot up into a much larger container to avoid doing it again, but oversized pots hold more moisture than young roots can use up quickly, creating conditions for root rot.
Using garden soil or heavy potting mix.
Garden soil compacts in containers, drains poorly, and can harbor disease. Conversely, seed starting mix is too light and nutrient-poor for growing seedlings. Use a quality potting mix instead.
Handling seedlings by the stem.
Even gentle pressure on a seedling’s stem can crush the vascular tissue that moves water and nutrients through the plant. Hold by a leaf instead. Leaves are replaceable, stems are not.
Skipping the pre-watering.
Trying to remove a dry root ball often means it crumbles apart, leaving roots exposed and vulnerable. Water an hour or even right before you start and the whole process goes much more smoothly.
Fertilizing immediately after potting up.
Fresh potting mix already contains nutrients, and a seedling that has just had its roots disturbed is not in a good position to take up fertilizer efficiently. Wait a couple weeks, then resume your normal fertilizing routine.
Your Turn to Grow
Potting up is one of those skills that feels nerve-wracking the first time and more and more intuitive by the third season and beyond.
For me, the first year of seed starting was the hardest. I was learning to read my plants and trust my instincts at the same time.
Keep at it, and before long you’ll be glancing at a tray of seedlings and just knowing it’s time to move them up.
One last reminder: indoor-grown seedlings always need to be hardened off before they go outside, no matter how strong they look.
A plant raised under grow lights has never experienced wind, rain, or direct sunshine. They need to be introduced gradually.
Here’s how to harden off seedlings if you need a refresher before transplant time.