This guide is designed to help you achieve germination success when starting vegetable seeds indoors. It is one guide in a series of videos and articles to help you grow your own food.

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

My first three years of starting seeds in my small shop were rather angst-ridden.  I was depending on selling hundreds of plants at market 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.

This is what I have learned over the years. Hopefully it will help you on your journey to grow your own food. Two videos are included to further help.

Methods & Set-up 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:

I.      The Germination Process

II.     The Seedling Growth Stage

Caveat:  I grow around five thousand heirloom tomato and pepper seeds each year now, so these vegetables are my focus. The principles and methods of seed starting are the same for most seeds however, with variations in the time it takes 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 to grow on in pots (here is a good post on growing tomatoes in containers).

I.  The Germination Process

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

Useful seed starting supplies
Useful seed starting supplies

1)  Timing:  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 if you are growing tomatoes (read the seed package for other seed germination times) 

In Central Minnesota, where I live (Zone 4), 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 spent too much energy forming those blossoms, leaving them somewhat depleted and hence not able to yield as many tomatoes.

2)  “Soil” for seeding:  If you are a totally organic grower, you can make your own potting mix (but it is a bit involved).  I have tried several, but my favorite combination is as follows (you will need to scale down proportionally for smaller batches):

  • 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)

If you’re not worried about being totally organic, Miracle-Gro Moisture Control is a potting soil that gives consistently good results.  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.  Garden soil carries disease-promoting fungi that is hard on young seedlings, not to mention the weed seeds prevalent in garden soil.

3)  Trays/Flats/Containers:  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.  Larger seeds (like squash) would need flats with larger cells (I use 98-cell flats for large 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. 

It is worse for the container to be over-watered rather than under-watered (that damping off condition again).  *Note:  if you are using a grow light setup similar to mine, make sure your bottom tray that the cells sit in does not have holes in it or it will drain onto the grow lights below and short them out.

4)  Seeding Process:

Potting Mix Moisture Level
Potting Mix Moisture Level
  • 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.
  • 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.
  • 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).
  • 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.
  • 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.
Using 100-watt bulbs for heat source under seed germination trays
Using 100-watt bulbs for heat source under seed germination trays

4)  Heat Source: 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 during germination, but the main heat source for the soil is 100 watt bulbs placed under the 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. 

I do check the flats once a day and mist 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. 

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.

5)  Watering/Misting:  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 the damping off situation described above. 

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 coiled hose attached to my shop sink. 

The indoor hose pictured below is no longer available and I have switched to the  is a Water Right MCH-050-FG-6PKRS 50-Foot x 1/4-Inch Mini Coil Hose With Wand – Forest Green, which has a small nozzle, and it is perfect for misting the seeds at this stage and watering the seedlings with a larger stream of water later on.  I love this hose, but it does get clogged occasionally with the minerals in our water (we’re on well water) and needs to be cleaned regularly.

Indoor garden hose for watering small seedlings
Indoor garden hose for watering small seedlings

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 the Step by Step Video for More Details

Now the next stage – the seedling phase

II.     The Seedling Growth Stage

Front view of indoor seed starting setup
Front view of indoor seed starting setup

1)  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.
Light set-up over tomato and pepper seedlings
Light set-up over pepper and tomato seedlings

2)  Day and Night Temperatures:  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.

3) Watering:  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 and should be watered gently. 

4) 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 growing in flats
Thinning tomato seedlings growing in flats

5)  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 table fan will work fine also. 

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!

6) Re-potting:  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. The store plants have long since outgrown their small containers.  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. 

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 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.

7) It is important to trouble shoot problems and disease signs while the seedlings are in this stage and vulnerable. Click here for a post on some typical disease solutions. Keep the re-potted plants out of bright sunlight for a few days so they can ease into the transition. 

The next stage before planting in the ground is Hardening Off. Here is a link to the video on hardening off.

Comments are welcomed.  Share your tips and tricks, or questions. I try to answer all questions via video or in the comments.


  1. tarry on May 13, 2016 at 2:04 pm

    best for sanwich

  2. susan on May 2, 2016 at 5:16 pm

    When is the next posting. I think I’m ready for Hardening off.

  3. Marie on March 2, 2016 at 2:30 pm

    Absolutely love the blog! It was a revelation for me that you’re not using expensive grow lights since I can’t seem to find anyone else who uses them. I know someone else left a comment earlier asking about the lights but no specifics were mentioned. It would be great to know which t lamps you are using since everyone else seem to think that those lamps other than t12 are not efficient for growing. The t12 are definitely on the expensive side since they need ballasts. Do you have one in a box lying around that you could post a picture of or even just let us know the information on it.

    Thank you!

    • Dorothy Stainbrook on May 5, 2016 at 6:55 pm

      I just use the basic variety that you get from Walmart that fit the shop light fixture. I use one cool and one warm in each shop light.

  4. Shirley Curnel on March 30, 2015 at 1:37 pm

    Hello, we have heirloom seeds from large German tomatoes and have started seedlings indoors with a grow light as we did last year with great success. This time we are having a problem with entire plants disappearing after they reached 3-4 inches tall. The plants are in flats located near but not touching basil plants and a Philodendron. The other plants were not harmed. We thought maybe mice, but have found no droppings or other indications and there are 4 cats living outdoors around the house. Is there anything else we should be looking for? Maybe a parasite in the starter mix? Thanks for any help you can provide.

    • Dorothy Stainbrook on May 11, 2015 at 6:21 am

      Shirley, the only thing I know of that makes larger plants disappear totally is some kind of chimpmunk or animal pest. I don’t know much about parasites. If they are too cold and damp they might get root rot and die, but you would probably see some sign of the plant.

  5. Sara Wilson on March 22, 2015 at 8:39 am

    Thank you for your excellent article! This is our second year gardening and we tend to jump into things with both feet. I am trying to grow enough to feed our family of 6 (fresh and canned tomatoes) for the year. Where do you find the cool/hot lights? We can only find grow lights online. We bought T5 lights at Home Depot. It came with two 3000k bulbs, 2280 lumens. We looked all over Home Depot. So confused!! HELP! =))

    • Dorothy Stainbrook on May 11, 2015 at 6:22 am

      I just get my lights at either Walmart or Menards. They might say something a little different than “warm” and “cool” depending on brand.

  6. march gardening chores | Decker Rd. Seeds on March 10, 2015 at 11:39 pm

    […] little bit before you stick them outside for good.  For a great seed starting tutorial, check out Tomato Headquarters site.  Probably the best guide I’ve ever read, so I figure you can read it there instead of […]

  7. Domates Tohumu on April 25, 2014 at 4:49 am

    Dear Dorothy,
    Is there anywebsite that i can order heirloom tomato seeds ? Thank you in advance.

    • Dorothy Stainbrook on April 25, 2014 at 5:21 am

      Domates, in the search bar of this blog type in “seed catalogs” and it will show you my top 5 favorite catalogs for ordering heirloom tomato seed and why. You can start with as they probably have the most. A lot of theirs are hybrids also however.

  8. Jacqueline on April 21, 2014 at 8:10 pm

    I have read lots of websites and yours is so well detailed. Thanks for all the great information. I have one question that I have found the answer… Once you place the seedlings under the grow light how long should they stay under 1 month, two weeks, etc. Your answer would be appreciated. JP

    • Dorothy Stainbrook on April 22, 2014 at 6:07 am

      Jacqueline, Basically they need to stay under the lights until they have their second set of true leaves or until the weather permits them to be hardened off. They are not under the lights for 24 hours. I keep them under lights for about 15 hours a day when very young and back off after they get larger.

  9. joanne on February 19, 2014 at 1:02 pm

    thank you for your knowledge I am new to this all its a new adventure for me im excited but nervous at the same time soil with your experience the soil could I use a name brand? OR your combination would be the best for a beginner u did say moisture control would work iam planning to do 500 plants your recepie is for how many? where would you buy heirloom seeds from what company? lots of questions here ;] thanks a bunch joeeeezz

    • Dorothy Stainbrook on February 20, 2014 at 11:10 am

      Joanne, Miracle Grow Moisture Control is a good brand. I have a post on my site regarding where I purchase seeds. Just use the search bar and type in seed catalogs and there is a comprehensive review.

  10. Anonymous on January 20, 2014 at 4:30 am

    Wonderful information. Thank you for sharing what worked for you.

  11. […] the standard charts predict by placing bottom heat under my flats using 100-watt light bulbs (see this post for my seed-starting setup).  A nice infographic on the relationship between temperature and […]

  12. Cstainbrook on March 20, 2012 at 11:41 pm

    you should also note that the plants need to be in an area free of all critters.

    • heathglen on March 21, 2012 at 8:00 am

       Definitely!  My first year of starting seeds in the shop I lost several flats of seedlings when the young leaves disappeared, leaving a bunch of small straight stems.  It took a while to figure it out, but it turns out mice were nipping off the leaves at night. 

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