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How to Grow Peppers from Seed

Of all the vegetables that can be started indoors, peppers seem to offer gardeners the most challenges. Each spring, we receive a number of emails from distressed gardeners who can’t figure out why their pepper seeds haven’t germinated. They planted them, watered, and waited and nothing happened. If you’ve arrived at this article in the same situation, don’t be discouraged. A lot of garden experiments require replication (my preferred word over “starting over”). This article is designed to give you a step-by-step guide on how to successfully start peppers from seed, every time.

Bunch of peppers

Factors That Affect Pepper Germination

There are a number of factors that will affect the germination rate of your pepper seeds. If you are reading this article with a packet of seeds in your hand and the scent of fresh soil permeating the air, I’m sure you will be tempted to scroll past this section and get down to business, but I assure you that a acquiring a little bit of understanding about pepper seed germination now will pay dividends in the future.

Pepper seeds

Seed Quality

It’s no surprise that the quality of the seed is the most important factor in determining the outcome of germination. Under the Federal Seed Act, the minimum germination rate for peppers sold in the United States is 55%. That leaves a lot of room for variation, and you will undoubtedly see differences in germination rates if you purchase seeds from different sources. Therefore, it is important that you start with high quality seeds from a reputable source. At Thresh Seed Co., our pepper seeds average around 90% germination, with above-standard rates maintained for 2-3 years thanks to our moisture and light-proof, resealable packaging.

Variegated peppers


To some extent, the genetics of a variety will determine its potential for germination. We have observed, for example, that “Fish” pepper seeds tend to have an inherently lower germination rate. I suspect that this is due to the variegation within the maternal tissues of the developing fruit, though I've never investigated it fully. Whatever the case, you may sometimes find that a certain variety has an inherent limitation on germination rate.

Pepper germination time by soil temperature

Soil Temperature

Apart from the innate germination potential of the seed, the next most important factor influencing germination rates is soil temperature. The optimal soil temperature for pepper seed germination as prescribed by the Association of Official Seed Analysts (AOSA), is 85 degrees Fahrenheit. The following graph shows the average germination of pepper seeds over time using the AOSA protocol (green line). In the same graph, you can see how lowering the soil temperature increases the days to germination and decreases the overall germination rate.

The influence of soil temperature on the speed and rate of germination is worth noting because most gardeners do not have access to a temperature-controlled greenhouse, so they settle for the next best place—a window sill. A window, preferably south-facing, can be an excellent place to start your seeds. However, care should be taken to protect the germinating seeds from drafts and cold temperatures at night. Placing a seedling heat mat beneath the trays can vastly improve germination rates by keeping soil temps warm and stable. They can be purchased for as little as $15 online and they will last for years. Although a heat mat will improve germination of most vegetable seeds, we think they are especially critical for starting peppers and we recommend them to all of our customers who are wanting to grow their own peppers.

shishito peppers


Over-watering is the most common mistake when starting peppers, or any seed for that matter. When it comes to peppers and water, less is more. Watering the plants cools the soil and invites fungal growth. Additionally, most tap water contains small microbes that can grow in the soil. As peppers are somewhat slow to germinate, any competition with fungi or other microbes hurts the seeds' chances of germination. Furthermore, certain fungi can cause “damping off” a fungal disease that is often deadly for seedlings.

 What is damping off?
"Damping off" is a general term used to describe the sudden death of seedlings during or shortly after germination. Damping off is most often caused by fungal pathogens and its prevalence and severity is heavily influenced by soil conditions. Cool, water-logged soils are most prone to damping off as these conditions are favorable for fungal growth. The gardener's goal when starting seeds, therefore, is to get them up and out of the soil as quickly as possible. Once the seedlings are sufficiently large to resist fungal growth, they will no longer be susceptible to the fungi that cause damping off.

datil peppers

Soil type

Shopping for soil can be confusing. There are a lot of different kinds and the labeling can be ambiguous. In general, avoid anything labeled as Top Soil or Garden Soil. The mixture you are looking for is actually soil-less, although it may still be labeled as “Soil”. See, I told you it was confusing. When in doubt, look at the ingredients. Avoid soils that contain compost, manure, or natural soil. They likely are not sterile and may introduce fungi or other microbes. Instead, look for soils that contain a combination of peat, bark or coconut, and perlite or vermiculite. If you are blessed to have a local garden center, you may even be able to find a product labeled as seed starting mix. Seed starting mix is a sterile, soilless mix that has been run through a screen to remove larger chunks of organic matter. It may also contain wetting agents that help the water penetrate the soil without running off.

The last thing to look for in your soil mix is some sort of calcium. Calcium seems to improve germination rates under various kinds of stress (Mulaudzi et al. 2020) and most importantly, it cannot be conveniently added later (in liquid form). Therefore, you want to be sure calcium is in the soil from the start. Most growing mixes will have some sort of calcium source, usually lime (Calcium Carbonate, CaCO3) or dolomite lime (CaCO3 with significant amounts of MgCO3). Less common sources of calcium include oyster shell, ground marble, or gypsum.

ozark giant bell pepper

How to Grow Peppers from Seed

Okay, we're ready to get started. Time to gather up your supplies. Below is a list of the items you will need. If any of them sound surprising, refer to the section above.

You Will Need:

  • Seed trays and dividers
  • Clear plastic dome
  • Seedling heat mat
  • Sterile seed starting mix
  • Watering can
  • Pepper seeds
  • Planting stakes for labeling
  • Natural or artificial light source

Step by Step Instructions:

planting trays and dividers

Step 1.  Sterilize trays and dividers

If you are re-using old trays or dividers, be sure to sterilize them by scrubbing with hot, soapy water. Soil that has been left in the trays could be harboring soil pathogens that may threaten your fragile seedlings.

trays filled with soil mix

Step 2. Fill trays with soil mix

Use a sterile, soilless starting mix (see section above). Pile the soil in the center of the tray. Break up the clumps and remove any large chunks of bark or wood that may be in the soil. Smooth the soil out to the edges until all of the cells are filled and the soil level is flush with the tops of the containers. The level will decrease slightly after watering.

pre-moistened seed starting mix

Step 3. Pre-wet the soil and allow it to drain

If you are working inside, it may be best to do this outdoors. You want to put a good bit of water through the soil to make sure it is completely moistened. Allow the soil to drain for at least 15 minutes. For best results, repeat.

making soil depressions with finger

Step 4. Make an indentation in the soil

Using your finger, make a ¼ inch indentation in the soil. For reference, ¼ inch is roughly half-way to your first knuckle. If you have a good soil mix and optimal moisture, your finger should press easily into the soil, like pushing on a soft sponge, however the soil should not rebound when you remove your finger.

sowing pepper seeds

Step 5. Sow the seeds and cover

Sow 1-2 seeds into each hole. You can either pinch in the soil around the hole or add additional fresh mix over the top. If you are planting multiple varieties, label each with a stake or popsicle stick. Also include the sowing date.

Step 6. Water once more

Once again, you want to soak the trays. Water until you can see water draining from the bottom and then water a few seconds longer. Allow the tray to drain completely. You do not want any water sitting in the bottom of the tray.

Step 7. Place the tray on a grower's heat mat

Don't forget to plug in the mat. If your mat has a probe, place it in the soil and set the thermostat to 85 degrees. Simple mats without this feature work just fine too.

starting peppers with heat mat and plastic dome

Step 8. Place on a heat mat and cover with a plastic dome

Using a dome helps to keep the soil warm while minimizing the need for watering. It also protects young seedlings from cold air and drafts.

venting a plastic dome

Step 9. Watch and wait

I know, it's hard. Keep in mind that you likely will not see any sprouts for a week or two. Many gardeners sow tomatoes and peppers at the same time and begin to get anxious when they see tomatoes germinating after just a few days. Try to be patient, peppers just take a little longer.

This is the biggest secret to starting pepper seeds: Do not water the plants for at least two weeks. Every few days, you can tap the top of the lid to redistribute the water that has condensed inside and lift the corner to let in a bit of fresh air. If the temperature in the growing room gets particularly hot, for example if you are using a sunroom, prop up the corner of the lid using a pencil. Always close the lid at night, though. This will keep the soil warm and the seeds growing throughout the cooler nighttime hours.

pepper seedlings

Okay, they're up! Now what?

Well done! Congratulations, the hardest part is over. After most of the seeds have germinated, you can remove the lid and unplug the heat mat. The seedlings will need cooler temperatures now--room temperature is perfect. If temperatures are too high, the plants will grow too quickly, causing them to become soft and tender, thus making their transition to outdoor living more perilous. Keep the seedlings under light or near a south-facing window. Plants that do not get enough light will stretch looking for it, causing them to become leggy and fragile.

When to Water Pepper Seedlings

Wait, don't water yet! If you've just removed the dome, chances are the seedlings still have plenty of water. Keep in mind that the chili pepper likely originated from central Mexico, where it almost certainly experienced extended periods of drought. Watch your plants and trays and look for signs that the soil is getting dry. On the outer edges of the tray, the soil may begin to pull away from the container walls or the leaves may begin to droop. If this happens, then by all means, water. If you are going to be away for several hours and you know the plants will get thirsty, then water pre-emptively. The goal is to give the plants enough water, while allowing the soil surface to dry between waterings. If the soil surface remains wet, algae and fungi will begin to grow on the soil surface, creating a thick algal or fungal mat that prevents water absorption.

Despite our best efforts, some algal and fungal growth is common. If it becomes such a problem that water is running off the top of the top of the soil and down the sides of the container without penetrating the soil, it may be time to intervene. Gently scrape the top of the soil with a fork to break up the crust. Don't go so deep as to damage the roots, just rough it up a bit to create a path for water to enter.

When to Fertilize Peppers

Seeds are amazing creations. Inside each one is the beginnings of a plant-- a root, a shoot and the first few leaves-- as well as enough food to get them off to a good start. Therefore, you do not need to fertilize your seedlings at first. If fact, doing so may be of more benefit to soil pathogens than it is to the seedling. Should you choose to fertilize your seedlings, it is best to wait until the plants are large enough to resist fungal diseases-- this is usually once the first set of true leaves is fully emerged. We seldom fertilize our seedlings unless we notice that the leaves are getting a bit pale. At this point, we'll give them a half-dose of liquid fertilizer and see how they perform. If their condition improves, we'll give them another half-dose a week later.

Woohoo, You Did It!

If you made it this far, congratulations! Your seedlings are getting close to being able to move outdoors. Until the weather improves, the key is just to keep them healthy. Pepper plants have a tendency to grow fairly slowly during the first month of growth, so don't be alarmed if you don't see much progress. They're just getting ready to take off. In the meantime, feel free check out some of our other articles on gardening and stay tuned for our next article about how to harden off and transplant your pepper seedlings.


Becky Weeks

Becky Weeks

2 Responses



May 03, 2021

Hi Cheryl. Once the plants have a couple sets of true leaves (~2 weeks after sprouting), it is safe to apply a liquid fertilizer. We use Miracle Gro’s all purpose plant food (24-8-16 NPK) for this stage, but I’m sure there are other good options. We usually apply the fertilizer at half rate, wait a week and then apply again. This prevents the plants from becoming soft, which can happen if too much fertilizer is applied at once. Weekly or biweekly applications can be made at half rate until flowering, at which time it is best to switch to a fertilizer that has less nitrogen and more phosphorus in order to encourage fruit set.



May 03, 2021

Thanks for the info about starting peppers indoors! Mine have come up and I’m wondering what type of liquid fertizilier to use when it’s time? Thanks.

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