Skip to Content

Ultimate Guide for Starting Tomatoes & Peppers Indoors From Seed

Ultimate Guide for Starting Tomatoes & Peppers Indoors From Seed
Home » Grow Your Own Food » Growing Great Tomatoes » Starting tomatoes from seed

My first three years of starting seeds in my small shop were rather angst-ridden.  I was depending on selling hundreds of plants at the farmers’ markets and I had never done anything like this before. I read, and watched, and worried, and called the seed companies and MN Extension Service ad-nauseum.

In this article I share my inexpensive seed starting set-up, germination tips and how to grow the seedlings on once germinated.

Follow along to see if there are any ideas that inspire you to start your own seed this year!

Flat of 4-week old pepper seedlings
Flat of 4-week old pepper seedlings

Jump to: Good Potting Soils | Containers for Starting Seeds | Step by Step for Germination | Heat Source | Watering | Grow Light Set-up | Growing Tips for Seedlings | Potting up | Hardening off

This post may contain affiliate links, and you can read our disclosure information here– 

Methods for Successful Germination and Growth

In this post I’ll  pass on some of what I have learned over the years , in hopes that it will help you on your way to growing healthy plants in your garden or farm. 

It’s a lot of information, so I’ve organized this post into two main sections:

  1. The Germination Process
  2. The Seedling Growth Stage

Caveat:  I grow mostly heirloom tomato and pepper seeds, but the principles and methods of seed starting relate to most seed varieties. The variations are mainly in the time it takes different seed types to germinate. 

Of course, you will have to modify the size of your set-up if you are only starting a few seeds for a small garden or if you are starting seeds for the purpose of growing tomatoes in containers.

OK, let’s get started! Gather together the following items to get you on your way:

Helpful tools to use when starting your plants from seed. phone, plant tags, timer for lights, mini-clippers, sharpie, bread knife.
Equipment: seed packages, something to use for tags, pencil, knife, marker, small clippers, timer for lights, phone for music

I. The Germination Process

** Note: this post is focused on tomatoes and peppers, but with a few exceptions the information applies to most seeds.

Best Potting Soil for Seed Starting

If you are a totally organic grower, you can make your own potting mix (but it is a bit involved).  I have tried several recipes, but here is my favorite combination for organic DYI potting mix (you will need to scale down proportionally for smaller batches):

DIY Organic Potting Soil

  • 5 gal. compost
  • 5 gal. peat
  • 3 – 5  gal. mix of vermiculite & perlite
  • 1/2 c. lime (don’t use this if your compost is horse manure as the beds are often limed)
  • 1/2 c. bonemeal
  • 1/2 c. bloodmeal
  • 1/2 c. greensand (or 1/4 c. sul-po-mag)
Newly germinated tomato seeds
Newly germinated tomato seeds

Store-bought Potting Soil

If you’re not worried about being totally organic, Miracle-Gro Moisture Control is a potting soil that gives consistently good results. 

*Tip: The main thing to know is to use a sterile potting mix, not garden soil. 

Starting seeds in garden soil frequently leads to “damping off” of the seedlings, where they start to grow and then just keel over and collapse at the stem. 

Soil that comes straight from your garden often carries disease-promoting fungi that is hard on young seedlings, not to mention the weed seeds prevalent in garden soil.

Best containers for starting seed:

I use sturdy, reusable, 128-cell flats that have lasted a minimum of 5 years (and I am not gentle with my equipment). 

Any container will work, including yogurt cups, peat pots, etc. as long as there are holes in the bottom for drainage. Larger seeds (like squash seeds) would need flats with larger cells (I use 98-cell flats for large seeds)

12-pack seed plug tray, with squash seeds on the side.
12-pack seed plug tray for squash and larger seeds.

One of the reasons I start my seeds in flats with shallow cells is to fit as many seedlings as possible under the grow lights, but an equally important reason for me is that the seeds will germinate faster in smaller shallow cells. 

The small amount of potting mix in each cell heats up more quickly, and there is not as much of a danger of over-watering. 

Pro Tip: It is worse for the container to be over-watered rather than under-watered. Overwatering causes the condition of damping off which is fatal to seedlings.

Step by Step Seed Germination Method

These are the 5 key steps in getting your seeds to germinate (see video at end of article for a visual of this process):

  1. Pour your potting mix into a large, shallow tub.  Add hot water in increments and mix well with your hands.  Take a handful of the mix and squeeze.  You want the potting mix to be damp enough to form a ball, but not so wet that you can wring water out of it with a gentle squeeze.
  2. Fill the flat with the potting mix and then hold it slightly above the floor and let it drop to the ground to make sure the mix compacts a bit and gets into all the cells.  If the mix is too fluffy, the seed will not make good contact with the soil particles.  Refill any of the cells that are not full after dropping the flat.
  3. Mark the seed variety and the date on a small but sturdy tag (I use cut up venetian blinds I get at garage sales), and place the seeds on top of each cell individually.  Some people pour the seeds out carefully onto the cells, but it really doesn’t take that long to seed the cells individually (good time to listen to music or podcasts).
  4. Now go back to the first cell and use the pencil with one hand to poke the seed slightly down into the mix and use your other hand to firmly cover the seed with a small bit of the soil.  If you are only starting a few seeds, and using individual containers, don’t poke the seed down too far into the soil.  It just needs to be slightly covered. The general rule of thumb on sowing is the depth should be 3 times the size of the seed. The main thing is to make sure the seed has been firmly pressed into the soil.  Good contact with the soil is important to germination.
  5. Cover loosely with plastic to keep moisture in and the seeds warm.  The clear tops that come with some of the flats are fine, but you don’t really need them.  The plastic is only on the seeds for a few days and then you are done with it.  Easier to fold up a piece of plastic and store it for next year than store the hard plastic covers.
Example in hand of how wet potting soil should be when starting seeds.
Example in hand of how wet potting soil should be when starting seeds.

Heat source for seeds:

Warm soil is more important than warm air, which is why I use hot water when mixing up the soil. My seed-starting shop is not heated, so I do use a small electric heater to keep the ambient air around 70 degrees F during germination, but the main heat source for the soil is 100 watt bulbs placed under the trays.

Using 100-watt bulbs for heat source under seed germination trays.
Using 100-watt bulbs for heat source under seed germination trays

A  heating pad placed under the flat would work also, but these lights were something I had on hand 14 years ago and they worked so well I never found the need to upgrade.  The 100-watt bulbs put out quite a bit of directed heat and the seeds all germinate within 3 days. 

If you are only starting one flat or less of seeds, a seed starting heat mat works just fine.

I do check the flats once a day and sprinkle the cells with water if they look dry.  I will also turn the flats around if the germination is uneven.  Remember that germination time also depends on the seed variety and how old the seeds are. 

Tip: The date on the seed package is a packaging date, not the date the seed viability was tested.  Buy seeds from a credible company and don’t keep them over for too many years if you want 100 percent germination.

Watering “before” germination”

Seeds that are in the process of germinating  do not need a lot of water!  This is important because too much watering can lead to a condition called damping off which is usually fatal. 

The plastic sheets that cover the flats should be enough to keep the cells moist until germination, but you should check the edges of the flats often, as this is what tends to dry out first. 

I tend to keep the peppers on the dry side and the tomatoes a bit more moist.  When I do water them, it’s a very minimal gentle watering. I use a small watering spray wand attached to a hose which is attached to my shop sink. 

You’ve got seedlings!  If you are a visual learner and want to see video around these principles, here is a 5-min video on getting started.

Grow your own food - Tomato & Vegetable Seed Germination Tips & Tools
Watch this video on YouTube.
Watch the Step by Step Video for More Details

Now the next stage – the seedling phase

II. The Seedling Growth Stage

Grow Light Set-Up: 

My husband set up a grow light system for me that involves five 4-tiered metal shelving units with 20 fluorescent light fixtures attached to each shelf (see example above). 

Whether you have one light fixture or twenty, there are several key components to remember:

  • The distance between the light and the seedlings will change as they grow, so make sure the light can be easily adjusted up and down.  When the plants are very young, they will need to be fairly close to the light (about a 1-2 inch distance).  This is to ensure they do not get leggy and develop weak stems trying to reach for the light.  As they get bigger you can increase the distance so that the light source covers more area (around 4-6 inches distance).
  • Use two different types of fluorescent bulbs in the fixture; one warm bulb and one cool bulb.  You do not need to buy the expensive gro-light bulbs, the combination of warm and cool bulbs is really effective.
  • Keep the lights on the plants for 14-16 hours per day, but turn them off and let them rest at night.  A timer that you can plug the lights into is a must if you want to sleep peacefully.
Front view of indoor seed starting setup.
Front view of indoor seed starting setup

Day and Night Temperatures for Indoor Seedlings: 

Once germinated, I tend to grow my seedlings fairly cool to encourage slow steady growth that will give you sturdy, stocky plants. 

I keep the daytime temperature around 65 degrees and the night temperature around 55 degrees.  At this stage it is important not to have wide fluctuations in temperature.

Watering “after” germination

After the seeds have germinated but the plants are still very small, keep the soil moist, but not wet.  Seedlings will need more water at this stage than when germinating, but it is still important to have a light hand with watering.  The plants are still very tender.

Light set-up over tomato and pepper seedlings.
Light set-up over pepper and tomato seedlings

Note: If you are using a grow light setup similar to mine, make sure that the bottom tray that the plug tray sits in does not have holes in it or it will drain onto the grow lights below and short them out.

Thinning the seedlings:

Even if you have carefully hand-seeded, it is not uncommon to get 2-3 seeds germinate in one cell.  Make sure and snip off all but one (the straightest, strongest one) right at the soil line, so that they won’t compete for the same soil and water. 

It’s difficult to snip a seedling sometimes, but it is worth it.  Do it.

Thinning tomato seedlings with small scissors while growing in flats.
Thinning tomato seedlings growing in flats

Thinning seedlings will prevent legginess, a common problem in young tomatoes.

Air flow: 

Some of the literature recommends running your hands across tomato seedlings periodically, tickling them, to make the plants stronger.  A fan works much better.  An overhead fan is ideal, but a floor fan or a small table fan will work fine also. 

Inexpensive shop fan
Inexpensive shop fan

Keep it blowing across the seedlings for most of the day and turn it off at night.  It really does wonders for the strength of the plants.  They must think they are outside in the gentle breeze of spring.  Just don’t let them experience the roiling  thunderstorms of spring at this stage of their growth!

Potting up seedlings

This is really important, and a big reason why your home-seeded plants will be healthier than the plants you often see for sale at various stores, especially later in the season.

Often the plants available in the home stores have long since outgrown their small containers, especially if you are buying late in the spring.

When the seedlings are 3-4 inches tall and have their second pair of leaves, it is time to gently take them out of their cell and move to a larger pot. 

Tomato seedlings in 4” pots ready to plant out
Tomato seedlings in 4” pots ready to plant out

I use a dull kitchen knife to slide down the side of a cell and pop the plug out without disturbing the roots.  I pot them up into a 4-inch pot filled with more of the same potting mix that you used for germination. 

If your seedlings have become leggy, plant them a little deeper in the pot, but do not cover the green seed leaves, as they are needed to provide energy. 

Water the plugs well “before” you repot so the soil will stick to the roots and protect them from drying out.

Keep the re-potted plants out of bright sunlight for a few days so they can ease into the transition. 

Diagnose any early diseases:

It is important to trouble shoot problems and disease signs while the seedlings are in this stage and vulnerable. Typical diseases for seedlings are different than the diseases you will see later on. They are easier to remedy at this stage.

Tomato disease chart
Tomato disease chart

Before planting in the ground be sure to harden off your young seedlings in small steps. This stage is important to prevent them from wilting in the outdoor elements after being babied indoors.

Here is a video on hardening off if you prefer video over text.

Tomatoes hardening off outside
Tomato seedlings hardening off outside

How long after germination before seedlings can go outside?

It takes about 6 weeks for a tomato seedling to reach optimum growth for planting outside (about 8 weeks for peppers). 

So, wherever you live, determine when your weather is likely to be stable enough to plant in the ground and count 6 weeks back from that date before starting your seeds.

In Central Minnesota, where I live (Zone 4-5), I start all of my tomatoes March 14th through March 16th, and I start the peppers about 2 weeks before that. 

In mid-May, after they have been hardened off thoroughly, they are primed to get in the ground and start doing what they are destined to do….grow.

It is important that your seedlings be at the optimum stage of growth when you plant them outside.  This means stocky plants, with thick stems, about 5-9 inches tall, with good root growth (preferably having been potted up to 4-inch pots so they are not root-bound). 

You do not want tall thin plants with weak stems, because they will not transplant well. 

Nor do you want huge plants in small pots that already have blossoms on them, because this means they have already spent a lot of energy forming those blossoms, leaving them somewhat depleted and hence not able to yield as many tomatoes.

Flat of 4-week old pepper seedlings
Flat of 4-week old pepper seedlings

If you like my articles about cooking and gardening, subscribe to my weekly newsletter, where I share free recipes and gardening tutorials.

This site uses Akismet to reduce spam. Learn how your comment data is processed.


Wednesday 17th of January 2024

Brilliant…absolutely brilliant. Historically, trial and error has sucked the enthusiasm out of me as the seedling topple over perish. Your in-depth tutorial highlighted the error of my ways and provided appropriate corrections for my 2024 attempt! Thank you. You are indeed a Garden Oracle.

Dorothy Stainbrook

Wednesday 17th of January 2024

So happy I could help Valentina!! Love the term Garden Oracle!! Might have to use that somewhere in the future. Thanks for commenting!


Friday 14th of July 2023

My father used to sterilise the soil by placing a tray of soil in the oven to cook the soil to kill all fungus etc before putting the seeds in he always got 100% germination

Dorothy Stainbrook

Sunday 16th of July 2023

Yes, I suppose that would work, but if you’re starting very many seeds that could get messy and time consuming pretty quickly. If you buy potting soil it has already been sterilized. Same with if you are making your own mixture from purchased vermiculite etc. The only time potting soil wouldn’t be sterile is if you are using soil from your garden for example.


Tuesday 11th of April 2023

Thanks Dorothy, your info is realistic and feels like good advice rather than a fluffy commercial article. You've answered many of the questions I have! I'm using a grow light for my seedlings (just sprouted about 4-5 days ago) and I'm afraid they might grow too tall and skinny, so I was trying to find out how much time they should be under lights. I love your advice about having a fan flowing for air circulation too!


Wednesday 12th of April 2023

@dorothy stainbrook, Oh I didn't know that having the lights too far made them leggy, that totally makes sense! I just lowered my lights, I had them 18" over the seedlings.Thank you!

dorothy stainbrook

Wednesday 12th of April 2023

Hi Nancy, the best ratio for the seedlings to be under the lights is for 16 hours under lights and the rest of the time dark. Just make sure the lights are fairly close to the seedlings and that will prevent them from getting tall and skinny. Most tomato plants get leggy because they are reaching for the light so having the light source close to them is what helps.

Helen Bunch

Tuesday 28th of March 2023

I have been cross referencing so many videos, websites, and books, it has become in a muddle.....Your article is the best!...Taking us through the whole process, answering the questions that I have been wondering on.... Thank you!


Tuesday 11th of April 2023

@Helen Bunch, I agree! Got it bookmarked because I will keep referring back :)

dorothy stainbrook

Tuesday 28th of March 2023

Thank you so much Helen! I love getting feedback to know if my posts are helping people or if there is something more I can add. Appreciate you taking the time to comment!


Friday 13th of May 2016

best for sanwich

This site uses Akismet to reduce spam. Learn how your comment data is processed.