What to Do after Seeds Sprout & How to Care for Your Pepper Seedlings

Wondering what to do after seeds sprout? And why can pepper seedlings take so long to grow? In this detailed guide, you’ll learn how to care for pepper sprouts indoors so that they grow into thriving plants. Let’s get into all the specifics so you know exactly what to do during these early plant stages.

pepper seedlings

No matter how many years I’ve been gardening, I always find it exciting when seeds germinate. When you get your seeds to sprout for the first time, it’s common to ask yourself, So now what?

If you’re new to growing peppers, I have to warn you that the seedling stage can be tough! These young pepper sprouts have specific light, fertilizer, water and transplanting requirements to grow well.

But, don’t worry… this guide explains the ins and outs of what to do after germinating pepper seeds indoors. (You can also use this information for other warm-season crops like tomatoes and eggplants.)

Let’s get started!

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What You’ll Need

These are the growing supplies that you’ll need to take care of your pepper sprouts indoors.

What Do I Do After My Seeds Sprout Indoors?

what to do after seeds sprout indoors

Check your pepper seeds daily for germination because they’ll need attention after they sprout. Here’s what to do once your indoor seedlings are standing upright:

  1. Remove the humidity dome (lid). (See note)
  2. Unplug the heat mat 
  3. Put your indoor seedlings under the grow light

Removing the lid and heat mat keeps seedlings from getting too hot. Overly warm temperatures can make young plants grow tall and leggy (frail). These leggy seedlings turn into weak plants, and they can potentially fall over and never recover.

Note: Seedlings may react to the temperature difference of being uncovered. In this case, leave the lid on a few hours each day to help them adjust. Do this for just a few days, and then take the lid off permanently. 

grow tips

If your chile pepper seeds aren’t germinating, make sure the growing media isn’t dry and that the growing temperature is 80 to 90 degrees Fahrenheit (27 to 32 degrees Celsius). You can use a temperature controller with a heat mat to get into this range. Hot pepper seeds generally take longer to sprout than sweet pepper varieties.

How Do You Transfer Sprouted Seeds To Soil?

transferring pepper sprouts to soil

If you use the baggie method to start your pepper seeds, you’re probably wondering what to do after seeds germinate in the paper towel. Here’s how to transplant seedlings after germination to safely move them into their new pots.

Supplies Needed: Cell tray (or other containers), Seed-starting mix, Clean scissors

  1. Prepare your containers for planting in seed-starting mix.
  2. Cut a portion of the paper towel that has one pepper sprout. 
  3. Place the paper towel on top of the mix and cover it with another light layer of mix. (The seedling should be no more than ¼ inch away from the top.) Lightly spray water on top and you’re done!

The paper towel will decompose, and your pepper seedling will push through the mix as it establishes itself and continues growing in the pot.

grow tips

  • Use seed-starting mix as the “soil” when germinating seeds or transferring sprouted seeds from a towel. This mix provides the good airflow and drainage that emerging seedlings need. (You won’t need potting soil until you transfer pepper seedlings to larger pots.)
  • Alternatively, you can transfer sprouted seeds to media like peat pellets or Rapid Rooter plugs. Follow the preparation instructions on the package before planting your pepper seedlings.

When To Put Light On Germinated Seeds

when to put light on germinated seeds

After seeds germinate, put them under light immediately. Pepper seedlings grow fast, and they’ll need a grow light to replace the sun while they’re indoors. This lamp also keeps them from getting leggy because they won’t need to reach for a light source.

When it comes to choosing an indoor grow light, you can use something like a T5 fluorescent or LED. Below are some popular pepper light options (I have the Mars Hydro and love it!)

Grow Light Examples


Hydrofarm Agrobrite 4 Tube Grow Light

This T5 light system hangs over your plants. Comes in 2-foot and 4-foot sizes.


Mars Hydro TS-1000

Mars Hydro TS-1000W full spectrum LED grow light. Max coverage 3ft x 3ft.


Spider Farmer SF1000

Spider Farmer full spectrum LED grow light for indoor plants.

As far as the daily light schedule for seedlings, here’s what I recommend:

  • 16 hours ON during the day
  • 8 hours OFF at night

You can use a plant light timer to automatically turn your grow light on and off each day.

grow tips

Your grow light needs to be positioned at a specific distance away from your plants. Check the manufacturer’s instructions to get this grow light distance. (A T5 is typically 6 inches high, while an LED can be much higher.)

Should Seedlings Be Fed?

should seedlings be fed infographic

Pepper seedlings need to be fed after they grow a set of true leaves. These leaves — the ones that come after the embryonic cotyledons — are a visual cue that the young plant needs food to continue growing.

A good fertilizer for seedlings is worm castings or fish emulsion, which you’ll dilute at a ¼ strength for this growth stage.

Supplies Needed: Worm castings or Fish emulsion fertilizer

  1. Read the instructions on your fish/seaweed or worm tea fertilizer to determine what the ¼ strength measurement is. 
  2. Mix the ¼ strength fertilizer with the right amount of water. (Read the instructions on your fertilizer container to get this amount.)
  3. Pour the liquid in your plant tray so that the insert tray (or containers) absorb it from the bottom. Dump out any remaining liquid after the watering process is complete.
  4. Repeat this fertilization process weekly. 

Epsom Salt For Pepper Seedlings

In addition to weekly fertilizer, give your pepper seedlings magnesium sulfate (Epsom salt). This bonus supplement helps seedlings absorb nutrients and grow strong, green foliage. Give your plants a bimonthly foliar feeding after they have at least three sets of true leaves

How Often Do You Water Pepper Seedlings?

overwatered pepper seedling and dry seedling

The amount of water you give your pepper seedling depends on things like growing medium, container size and temperature.

So, should you water seedlings every day? It depends, as you may need to water once a day or every couple of days to keep the soil moist but not waterlogged.

Signs that your pepper seedlings need water:

  • The soil line is getting lighter in color. 
  • The container feels less heavy when you pick it up. (Be sure to pick up pots after you water your plants so you can tell the weight difference.)
  • If the pot is large enough, stick your finger down an inch of the soil to see if it feels dry. 

I recommend watering peppers from the bottom to properly hydrate seedlings. With this method, you pour water in a tray, and your plants get watered in reverse so that you know pepper roots are getting moisture.

You can also tell when seedlings have enough water because the top of the soil line darkens again.

grow tips

  • Keep notes when you water your seedlings to create a watering schedule. Do this again whenever you transplant pepper seedlings to larger pots.
  • Always drain any remaining liquid when you’re done watering your plants. Standing water creates a wet, humid environment that encourages pests like fungus gnats and diseases like damping off.

Thinning Pepper Seedlings

thinning pepper seedlings

It’s common to plant three pepper seeds in one pot to give you more chances that one of those seeds will germinate. If two or more seeds sprout, you’ll need to cut (thin) out these extra plants. 

Your seedlings should be at least an inch tall to make the thinning process easier. Choose the best-looking seedling to keep, and then use clean scissors to cut the extra plant(s) at the base where the stem and soil line meet.

It can feel awful cutting these baby pepper plants. However, if you don’t thin your seedlings, they won’t grow as well because they’re always going to be competing for things like water, nutrients and root space. These close quarters also increase the risk of disease. 

grow tips

I don’t recommend pulling your seedlings out by hand because the plant roots can grow intertwined. If you pull your seedlings, there’s the potential of also pulling out the plant you intend to keep. (I speak from experience!)

How To Keep Seedlings Alive

Chili pepper plants are sensitive in the seedling stage. Here are some common problems, along with how to prevent and fix these issues.

damping off banner

Problem: Damping Off

Symptoms: Seedlings have discolored seed leaves and thin stems; wilting and rotting of stem and roots below the soil

Prevention / Remedy: Keep trays and pots clean between plantings, start seeds in seed-start mix for good airflow and drainage, don’t overwater plants, provide a grow light

mold banner

Problem: Mold

Symptoms: Soil has fuzzy, white areas of growth

Prevention / Remedy: Run a small fan to provide better airflow, cut back on watering, scrape off mold, sprinkle a little cinnamon on the soil

leggy seedlings banner

Problem: Leggy Seedlings

Symptoms: Seedlings grow tall, weak and may fall over

Prevention / Remedy: Use a grow light or move your light closer to your plants

stunted growth banner

Problem: Stunted Growth

Symptoms: Seedlings fail to thrive and stop growing

Prevention / Remedy: Grow only one seedling per pot, try cutting back on water, feed your seedlings weekly, move your plants to larger pots, make the room temperature warmer (daytime 70F and night 65F, according to Cornell University)

not hardening off banner

Problem: Not Hardening Off Seedlings

Symptoms: Plants become weak, stop growing or die because they weren’t acclimated to the outdoors

Prevention / Remedy: Move peppers indoors again, and harden off pepper transplants before putting them back outside

Pepper Seedlings FAQs

What To Do Next?

I hope this guide clears up any questions on how to care for your pepper seedlings after they germinate.

Your next step is to move your pepper plants to larger pots. This transplanting pepper plants guide describes when and how to do this.

More In This Series:

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Jenny is the creator of Grow Hot Peppers. She is a self-taught gardener and has been growing peppers and a plethora of veggies for over 10 years. When she’s not writing or gardening, she loves eating spicy foods, hiking, and going to the ocean.

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