What to Do After Seeds Sprout: A Beginner’s Guide to Growing Strong Seedlings

Indoor seed starting gardening kit with biodegradable pots, soil discs, plant markers, and clear plastic humidity dome on a kitchen windowsill

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Starting seeds indoors is exciting. You plant them, keep them warm, and suddenly- tiny green sprouts appear! But what happens next? If you’re like me when I first started gardening, you might wonder:

When do I take the humidity dome off?
Should I turn off the heat mat?
What if two seedlings sprout in the same cell- do I toss one?
How do I make sure my seedlings grow strong and healthy?

I’ve made plenty of mistakes in the past, from leaving the covers on too long to overwatering my tiny seedlings. Over time, I’ve learned the best steps to take after seeds sprout to give them the best start. Here’s everything you need to know.

1. Remove the Humidity Dome or Plastic Cover

Indoor seed starting setup with seed trays, plant markers, and grow lights for beginner gardeners

When you first start seeds, you likely use a plastic cover or humidity dome to keep moisture in and create the perfect germination environment. But once you see sprouts, it’s time to take that cover off.

Leaving the humidity dome on too long can lead to mold, fungus, and damping-off disease (which causes seedlings to suddenly wilt and die). As soon as most of your seeds have sprouted, remove the cover to let air circulate.

2. Adjust the Heat Mat

A heat mat is great for germination because it keeps the soil warm, which helps seeds sprout faster. But once your seedlings are up, that extra heat isn’t needed anymore.

Turn off the heat mat once most of your seeds have germinated.
If you’re growing warm-weather plants like peppers or tomatoes, you can gradually wean them off the heat by running the mat only at night for a couple more days.

Letting your seedlings grow in slightly cooler temperatures (around 60-70°F) will prevent them from getting leggy and weak.

3. Move Seedlings to Proper Light

A collection of seed trays with humidity domes on a heat mat, illuminated by grow lights, indicating the process of starting seeds indoors.

This is one of the most important steps. Without enough light, seedlings stretch out too quickly, becoming tall and spindly instead of strong and sturdy.

If you’re using grow lights, keep them just 1-2 inches above the seedlings and leave them on for 14-16 hours a day.
If using a sunny window, make sure it gets direct light for most of the day. South-facing windows are best, but even then, seedlings might get leggy due to weak winter sunlight.

I’ve had the best success using grow lights. They make all the difference in keeping my seedlings healthy and stocky.

4. Thin Out Extra Seedlings

If you planted multiple seeds per cell or pot, you might now see more than one seedling sprouting in the same spot. This is where thinning comes in.

The best way to thin seedlings is to snip the weaker one at the base using scissors. This prevents disturbing the roots of the one you want to keep.
If you hate wasting a healthy seedling, you can carefully transplant it into another small container. Just be extra gentle with the roots. This is a riskier option.

It’s tempting to keep every sprout, but overcrowded seedlings will compete for nutrients and light, leading to weaker plants.

5. Watering Seedlings the Right Way

Now that your seedlings are growing, watering becomes important. But overwatering is one of the biggest mistakes new gardeners make.

Always check the soil before watering. If the top feels dry, it’s time to water. If it’s still damp, wait another day.
Bottom watering is best. This means adding water to the tray under your seedlings so they soak it up from below. It encourages deeper root growth and prevents mold.
If you have to water from above, do it gently with a spray bottle or watering can with a fine spout.

I used to overwater my seedlings, and they would get fungus and mold. Since switching to bottom watering, I rarely have issues.

6. Improve Air Circulation

Good airflow is essential to preventing diseases like damping off. I’ve lost so many seedlings in the past simply because I didn’t provide enough air movement.

Use a small fan on low near your seedlings to simulate natural wind and strengthen their stems.
If using a fan, rotate it so it doesn’t blow directly on the seedlings all the time.
Open a window occasionally (if temperatures allow) to bring in fresh air.

This simple step makes a huge difference in keeping your seedlings healthy.

7. Recognizing Cotyledons vs. True Leaves

Once your seedlings sprout, you’ll notice they have their first set of leaves. These are cotyledons, also called seed leaves.

Cotyledons don’t look like the plant’s real leaves. They are usually rounded or oval.
Their job is to store energy from the seed and help the seedling get started.
After a few days to a week, the true leaves will appear. These look more like the leaves of the mature plant.

Once true leaves grow, the seedling is officially past its most delicate stage.

8. When to Fertilize

Seedlings don’t need fertilizer right away because cotyledons provide the first nutrients. But once true leaves appear, it’s time to start feeding them.

Use a diluted liquid fertilizer (like fish emulsion or organic plant food- I use Fox Farm Big Bloom linked here) at half strength.
Fertilize about once a week to avoid burning the young plants.
If using compost or high-quality potting mix, you may not need extra fertilizer at all.

I usually start fertilizing around the two-week mark, and my seedlings always respond well.

9. Transplanting to Bigger Containers

As seedlings grow, their roots will need more space. If you notice roots poking out of the bottom of the tray or growth slowing down, it’s time to pot them up.

Transplant into a larger container once the seedlings have at least one set of true leaves.
Use a well-draining potting mix to avoid waterlogging.
Be gentle with the roots and avoid handling the stem too much.

Some plants, like tomatoes, actually benefit from being transplanted deeper into the soil, encouraging more root growth.

10. Preparing for Outdoor Planting

If you plan to move your seedlings outside, they need time to adjust. This process is called hardening off and prevents transplant shock.

Start by placing seedlings outside for a few hours each day in a sheltered spot.
Gradually increase their time outside over 7-10 days.
Avoid direct midday sun or strong winds at first.

I used to rush this step, and my seedlings would wilt the moment they hit the garden. Now, I take my time, and they transition much better.

Growing strong seedlings takes patience and a little know-how, but once you get the hang of it, it becomes second nature. The key steps to remember:

Remove humidity domes once seeds sprout.
Turn off the heat mat to prevent leggy growth.
Provide plenty of light (grow lights work best).
Thin seedlings to avoid overcrowding.
Water from the bottom and improve air circulation.
Start fertilizing once true leaves appear.
Transplant when needed and harden off before moving outdoors.

By following these steps, you’ll have healthy seedlings ready to thrive in your garden. Have you started seeds indoors before? Let me know how it’s going- I’d love to hear your experience!

With love,

Bri & Cat

Related Posts To Check Out:

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How to Start Seeds Indoors

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