10 Tips for Starting Pepper Seeds Indoors

It’s that time of year when we’re getting ready to start our pepper seeds indoors – wahoo! Whether you’re a first-timer or a seasoned pro, you’ll find something helpful in this article.

While peppers seem like a simple vegetable to grow, starting pepper seeds can be a bit tricky, especially when it comes to temperature. With a little planning and intention, your pepper plants will thank you with a bountiful summer harvest.

In this article, I’ll let you in on my top 10 tips for starting peppers from seed so you can confidently grow them. We’ll cover everything you need to know from soil mediums to when to transplant them outdoors.

Let’s go!

A photo of 6 pepper seedlings in a 6-cell starter tray

*Disclosure: This post may contain affiliate links to products (including Amazon). I’ll earn a small commission if you make a purchase through my link, at no additional cost to you! Regardless, I only link to products that I personally use on our homestead or believe in.

10 Tips for Starting Pepper Seeds Indoors

#1 Use fresh seeds

This one may seem obvious, but it’s an important place to start. If you only grow a few pepper plants each year, you may find that you still have extra seeds after a couple of years. Can you still use them?

Pepper seeds are too old to use once they hit 3 years. During the first 2 years, the seeds are still viable as long as they are stored properly

Pepper seeds on a white background

If your seeds are too old, I highly recommend shopping at High Mowing Seeds! They are my favorite online store for organic vegetable and herb seeds; I’ve been shopping there for close to a decade!

#2 Start pepper seeds at the right time

There is an art to the timing of starting your pepper seeds and it all comes down to what your location’s last frost date is. You can figure that out easily by visiting Almanac’s website and entering your zip code. The last frost date is the average last day that your area will experience a freeze; it is never a promise!

My last frost date is May 19th, however, peppers do not tolerate freezing temperatures well at all, so I shoot for the first week of June to be safe. I’d recommend adding at least a week to your last frost date, maybe two!

Now, pepper seeds should be started 8 weeks before you want to transplant them outside. Grab your calendar and count backward 8 weeks from the date you decided to transplant outdoors. For me, 8 weeks before June 1st is April 6th, so that is when I start my pepper seeds.

This last frost date is separate from what growing zone you are in. A growing zone refers to the lowest temperature that your area experiences. My location typically hits -30 to -35, so I’m in zone 3B. To find your growing zone, visit the USDA Plant Hardiness Zone

Plant Hardiness Zone Map

#3 Use sterile, clean containers that are the right size

Sterilizing your growing containers is an important step when starting any type of seed. Diseases and organisms can continue to live in last year’s containers, so cleaning them well will ensure that you are starting the year strong and disease-free.

How to clean seedling containers

  1. Rinse well with hot water until soil is no longer visible
  2. Soak in a sterilizing solution for 30 minutes
    1. Traditional solution: 1 part bleach to 9 parts water
    2. Alternative solution: diluted hydrogen peroxide or white vinegar
  3. Allow containers to dry completely, and preferably in the sun to add a second round of sterilization.

What size of containers to use

  1. Seeding: start in a standard 1.5” square pot 
  2. When their first true set of leaves appear: transplant into a 3.3” seedling pot. This size should be sufficient until it’s time to transplant outdoors.

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144 cells (24, 6-celled trays), which will fill two 10x20 "flats". Each cell measures 1.5" square by 2.25" deep. These are so versitile and can be used year after year! This is the exact set that I've been using.

I searched for a while before I found this PERFECT sized pot! These will neatly fill your 10x20" flats with no wasted space. Transplant your seedlings to these once they develop their first set of true leaves.

#4 Use the proper types of soil at the right time

When starting pepper seeds (or any type of seed!), it’s important to use a soilless seed-starting mix rather than straight garden soil. These mixes tend to be fine and light while maintaining moisture well; perfect for seed starting! Another plus is that these mixes are free from soilborne diseases, which ensures that your seedlings are off to a strong start.

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The perfect blend of peat moss, vermiculite and lime for starting your seeds. I've been using this mix since day one and have had fantastic results!

TIP: Once the seedling’s first set of true leaves appear, it’s time to transplant them into the larger 3.3” seedling pots. For these larger pots, mix a ⅓ portion of seed-starting mix, a ⅓ portion of compost and a ⅓ portion of your own garden soil. This will provide more nutrients for the growing seedling while also introducing it to your garden soil organisms.

#5 Plant pepper seeds at the correct depth

Place 2-3 pepper seeds ¼-½” apart in a 1.5” pot and cover with ¼” layer of seed-starting mix. I like to use 2-3 pepper seeds for several reasons. First, not all seeds will germinate, so using 2 seeds is good insurance that at least one will sprout. Second, not all seeds that germinate will end up being a strong seedling, so if they both sprout, you can pick the strongest one to continue.

2 pepper seeds placed in a 1.5" pot of soil

#6 Provide adequate light

While pepper seeds don’t require light for germination, adequate light is very important once the leaves appear. Pepper plants need a lot of light, so just placing them on a windowsill won’t be sufficient; especially if you’re a northern gardener like me. 

You will need to use a grow light set at 16 hours to provide the intensity that it needs. Ensure that the bulbs are placed 3” above the top of the seedlings. The light will need to be raised as the seedlings grow as well – don’t forget that step!

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This is the LED grow light that I use (I have 3 of them!) and it's amazing. I like that I can set it up anywhere and it will easily cover 2 growing trays (10"x20"); you could even cover 4 if you're good about rotating them.

If you're growing on a small scale, this is an excellent choice! It has adjustable legs so that it can extend as your plants grow. I use this one while my seeds are germinating and then move them to the big lights later on.

#7 Provide the perfect temperature zones

Peppers are pretty picky when it comes to temperature, so this is definitely a tip to pay attention to! While you can just let them go at room temperature the whole time, the certain temperature zones will improve your flower and fruit production later in the growing season.


Peppers require fairly high temperatures of 80-85 degrees to germinate quickly for a strong start. Since most of us don’t keep our homes that warm, using a heated seedling mat can help achieve this. 

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The VIVOSUN professional heat mat maintains sweet-spot temperatures around 68-86℉(20-30℃), which is perfect for start seeding and cutting propagation; Made of high-quality PVC material, it is wear-resistant and durable to use.

Hardening off

Once your pepper seedlings have developed their first set of true leaves and have been transplanted into the 3.3” pots, it’s time to drop the temperature. It’s ideal for your peppers to sit at 70 degrees during the day and 60 degrees at night. This is pretty close to room temperature, so you can often achieve this by simply removing the heated seedling mat.

Then, once your pepper plants have grown their third set of true leaves, it’s time to drop the temperature again to 55 degrees at night to get them prepared for the outdoors.

I’ve found this step is harder to achieve since a 55 degree area is harder to come by. Therefore, I try to move my tray of pepper plants outdoors anytime it’s a nice day (50-70 degrees) to help them acclimate this way. Remember to bring them in if it gets chilly at night!

#8 Water just enough

Peppers are fairly standard plants when it comes to water. They prefer to be evenly moist. While you can purchase soil probes to monitor the exact moisture level of your soil, I just use the “eyeball method.” Once the soil is looking semi-light in color, I know it’s time to water!

#9 Add fertilizer for strong growth

Peppers are heavy feeders of nitrogen, phosphorus, and potassium. Once a week, fertilize your pepper seedlings with a half-strength fertilizer. There are several organic options available on the market, but my favorite is fish fertilizer. For the product below, a mixture of 0.5 oz per gallon would be perfect. Be warned; it does stink!

The Homesteading RD's Product Picks

Organic, highly nutritional protein fertilizer made with naturally occurring enzymes present in fresh north atlantic fish. Slowly breaks down into basic compounds when added to soil and promotes the growth of beneficial bacteria.

#10 Transplant pepper plants at the right time

While you’ve already calculated your expected planting date in tip #2 above, that date is never a certainty. Be looking at your extended forecast to decide if your date is actually a good bet or not this year. Last frost dates are always an average – some years it’ll be done freezing weeks before, and others it will be weeks after.

I’ve definitely done the dreaded trip of shape to dig up all of my pepper plants to bring them back to the safety of the house during an ice storm. Not fun! 

I’d say it’s safe to plant as long as your 10-day extended forecast is showing that your lows are only dipping into the 50’s. Don’t rush it! Peppers love heat. To make them extra happy, use floating row covers or secure black plastic over your garden bed to warm up the soil ahead of time. 

Common Problems When Starting Pepper Seeds

Many pepper seedlings in a row

Pepper seeds are not germinating

There are 3 main reasons why your pepper seeds aren’t germinating

  • The pepper seeds are too old or not viable (stored improperly)
  • The temperature is wrong for germinating – either too low or too high
  • The pepper seeds were planted too deeply (only ¼” inch is required)

Temperature issues are the most common. If you are already using a seedling heat mat, take a temperature probe and insert it in the soil to make sure that the mat isn’t malfunctioning. A soil temperature of 80-85 degrees is ideal.

Peppers are infested with fungus gnats

Fungus gnats are not only annoying to have flying around, but they can damage the delicate roots of your pepper seedlings as well. This can result in stunted growth and even collapse of the plant.

If you notice fungus gnats, don’t panic! They are easy to get rid of by following the following tips:

  • Avoid overwatering – fungus gnat larvae need moist soil to thrive.
  • Soap and water spray – add a few drops of liquid soap to water and spray a thin layer over the soil every few days. This should kill any residual larvae.
  • Add sand on top of your soil – this prevents the adult gnats from laying more eggs in the soil.

Pepper seedlings are leggy

The most common reason for leggy pepper plants is insufficient light. This could be due to not using a grow light, or your grow light is placed too far away. For compact growth, your grow light should be positioned 3” above the top of your plants. 

Also, make sure that your grow light is powerful enough to properly fuel your plants. There are some tempting small “wand” looking ones on Amazon, but they just don’t have the juice that your plants need. Check out my grow light recommendations in tip #6 above!

Leaves are turning yellow

Unfortunately, pepper leaves can turn yellow due to many reasons, so this one can be a little more challenging to diagnose. There are 6 main reasons why this may be occurring:

  1. Overwatering
  2. Lack of nitrogen
  3. Nutrient deficiencies
  4. Disease
  5. Pest infestations
  6. Too little sunlight

Mold growth is appearing on the soil

Fungi love humid conditions. If you are noticing mold growth on the top of your soil, then the conditions are too wet. This can occur from watering too frequently, or you are using a humidity dome for too long. 

Humidity domes are great to use for very brief periods of time while seeds are germinating, but should be removed promptly to avoid mold growth. Try adding a sprinkle of cinnamon to combat mold and mildew growth!

Best Varieties of Pepper Seeds

When starting pepper seeds indoors, it’s important to invest in the right variety to meet your growing conditions and taste preferences. All of the varieties below I have personally grown and love! I know that you’ll love them, too!

Pepper seedlings in 3" pots in a group


  • King of the North Pepper – A well-rounded heirloom pepper that beats all the rest in speed by finishing in just 57 days! The peppers are slightly smaller than the hybrid peppers below, but they taste great.
  • Corno di Toro Pepper – This Italian pepper is worth the wait of 70 days; trust me! Rich color, deep flavor and vigorous growth. 
  • Early Jalapeno Hot PepperSmall, moderately spicy fruits with thick walls and finishes in 65 days. Compact plants are sturdy and work well in containers!
  • HMS Red Picnic Pepper – These are a favorite at our house! They have unbelievable sweetness and a rich complex flavor that are amazing for snacking on. Finishes in 60 days.


  • Sprinter F1 Sweet Pepper – A fast growing pepper that’s mature in 62 days! An excellent choice for those with short growing seasons. High resistance to the tobacco mosaic virus and blossom rot.
  • King Crimson Sweet Pepper – Another fast finisher that matures in 60 days. Has intermediate resistance to the cucumber mosaic virus.
  • Bastan F1 Poblano Pepper Thick-walled, medium-sized fruits are a glossy dark green, nearly black, maturing to a deep chocolate with mild heat. Plants have an upright habit with excellent leaf cover and concentrated fruit set; extremely high yielding. Matures in 65 days.

Bonus Tips for Starting Pepper Seeds

Brush your hand over the plants daily

Wind is a wonderful, natural tool for making small seedlings grow strong and stable. When seedlings are grown indoors, they lack this physical stimulation. Gently brush your hand over your established seedlings daily to encourage the stems to strengthen and prepare for the big outdoors.

Pinch off the first few blooms

Pepper plants are vigorous growers and will often send out a few flowers while they are still in their seedling pots indoors. While it can be tempting to get a headstart on peppers, pinch these off if they appear and up to a week after they have been planted outdoors. Doing so will encourage your plant to continue to grow rather than directing its energy into pepper production too early.

Close up photo of a pepper plant bloom

This is similar to the strategy of topping pepper plants, but a little different. To learn more about it, check out my article Topping Pepper Plants – Should You Do It?

Can I use pepper seeds from store bought peppers?

Possibly, but likely not. Most large operations use hybrid pepper varieties, and you cannot use those seeds for future plants as they will not breed true. Also, pepper seeds are best to gather for planting once the pepper is nearly over-ripe. Most peppers that you see in the store are picked while they are under-ripe to keep them as fresh as possible.

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Out of all of the veggies out there, starting pepper seeds is one of the trickiest, but if you follow my top 10 tips then you’ll do great! 

The biggest mistakes that I see beginners make is not utilizing high powered grow lights and not paying attention to their temperature needs during different phases of their growth. If you can at least focus on these two, then you’re on the right track!

Happy gardening, friends!

*The information above was referenced from personal experience and my all-time favorite gardening book The Vegetable Gardener’s Bible, unless otherwise specified.

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25 thoughts on “10 Tips for Starting Pepper Seeds Indoors”

  1. Recently learned my peppers seedlings are growing too close together! I should have read this before! 🙂 thanks for all the great tips!

  2. This year I used seeds from 2016-2017…I’m glad you put that tip first. I will subscribe for your content. I think I need it…lol.

    1. Yes to both and definitely to the grow light. Not using a high powered grow light is the biggest issue that I see in new gardeners and the seedlings end up leggy and weak.

  3. I brush my hand over all of my seedlings. I don’t know if I do that because I’ve read to do that before, or if I just like the way it feels… but I’ve been doing it for years.

    Question: Do you recommend soaking pepper seeds before planting?

    1. I’ve heard of people soaking their pepper seeds first to improve germination, but it’s not completely necessary. I’ve never done it before and it turns out fine!

      1. Yeah, we’ve never soaked them. I’m tempted to do an A/B test. Plant some without soaking them, and others after having been soaked just to see if the soaked seeds pop up faster.

  4. As someone who does indoor apartment gardening, I find this is a very informative blog.
    I am experiencing a lot of flies in my apt from the soil I purchased from Dollar Tree (a bad idea). A Tiktoker suggested adding hydrogen peroxide. it helped a lot. But I like your idea of adding soap and water.

    From my experience, proper soil is very important in gardening. I usually purchase Miracle grow. Never heard of the Jiffy brand you shared; hope to get it on Amazon. Thanks for sharing.

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