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Seed Germination with Seed Starting Indoors

Seed Germination with Seed Starting Indoors

Although there are many factors to consider in growing healthy plants from seed, getting seed germination in the first place can sometimes be tricky.  Whether you are growing in a large garden or pots for the balcony, the methods and tools for successful germination are similar.

Newly germinated tomato seeds
Newly germinated tomato seeds

**NOTE: A detailed video showing how to start seed is available at the end of this post.

1) Seed Viability Relative to Seed Germination:

  • Shelf life:  Tomato seeds tend to last much longer in storage than most other seeds (i.e., onions need to be purchased fresh every year).  Just make sure they were stored properly (cool & dry) and you should have around a 4-5 year shelf life for tomato seeds.  Pepper seeds are considered by most growers to have a 2-3 year shelf life.  Fedco seed company puts out an informative chart on saving seeds, which includes estimates of shelf life for a range of vegetable seeds.  Click here for Fedco chart.
  • Storage:  Humidity shortens the life of saved seeds more than any other aspect.  Make sure seeds have wintered over in a cool and dry environment (such as in a tightly sealed jar in the refrigerator or freezer).  Dry storage at less than 65 degrees F will give you good germination results.
  • Vigor:  A number of online gardening sites explain how to test a few of your seeds for germination before planting.  Just be aware that even if your older seeds germinate, if they are too old or shriveled they may have a scant supply of food stored in their endosperm and the plants may end up weak and/or stunted.

2)  Seed sowing tips:

Example of how soil should clump when preparing to germinate seeds
How soil should clump when preparing to plant tomato seeds
  • Potting soil can be fluffy with air and seeds need to make good contact with the soil in order to germinate.  Moisten your potting soil before placing it in the flat or container, drop the flat on the ground from a few inches above the floor to settle the soil into the container cells, and then make sure your seed makes direct contact with the soil.  I use a #2 pencil to lightly push the seed into the cell and then use the pencil to push a bit of soil over the seed with enough pressure to make sure it securely covered
  • Very fine seeds do not need to be covered, just press them lightly into the soil.  A few seeds need light for germination (check your seed packages for which ones).
  • General rule of thumb is to cover seed to a depth of three times their size.

3)   Water & Seed Germination:

  • Water must be available to the seeds in order for them to germinate, but some air must also reach the seed for it to absorb the oxygen it needs.  I mix my potting soil with very hot water until it is damp but not soaking wet.  A good test is to squeeze a fistful of your moistened soil, checking to see if only a few drops of water squeeze out rather than a stream.
  • Check your flats daily to make sure they have not completely dried out.  If they become too dry, moisten them gently with a spray bottle.  Peppers, however, do not like to germinate in wet soil so go light on the water.

4) Timing & Temperature:

  • The length of time it takes for your seeds to germinate is heavily related to soil temperature.  Tomato seeds should germinate within 5-6 days if you can keep the soil temperature around 80º F.  Peppers take a little longer with a little higher temperature (7-8 days at 85º F). Remember this is soil temperature, not ambient temperature.
  • Speeding things along:  I usually get germination earlier than the standard charts predict by placing bottom heat under my flats using 100-watt light bulbs (see this post for my seed-starting setup). 

5) Preventing disease following seed germination

Young seedlings are quite fragile in the weeks after germinating. This is when they are susceptible to root rot and getting leggy. Click here to read about preventing disease in tomato and pepper plants following seed germination.

Special Germination Tricks for Difficult Seeds

  • Pre-soaking seeds:  Soaking seeds in warm water overnight before planting helps to soften the seed coat and speed up germination.   Many seeds, even if it is not stated in their steps of seed germination, will benefit from pre-soaking.  I don’t usually pre-soak tomato and pepper seeds, but I always pre-soak parsley, sweet peas and nasturtium seeds
  • Scarifying seeds:  This refers to the process of literally damaging the seed coat, usually by scratching the seed with sandpaper and then soaking in water.  Some seeds (i.e., woody plants in the legume family) are so hard and well protected by their seed coat that the seedling is not able to break through it on its own.  Tomato and pepper seeds do not need scarifying, but some of the larger seeds with hard seed coats would benefit from this.

I have been starting tomato and pepper seeds for market now for over 15 years.  The book that I found to be most useful at the beginning of my adventure is The New Seed Starter’s Handbook, by Nancy Bubel.  This book is research-oriented, comprehensive, and provides the scientific rationale behind each method she promotes.  For more thorough information on the tips offered in this post, I would highly recommend Nancy Bubel’s book.

Seed starting and germination
Seed Starters Handbook
How to Grow Your Own Food - Seed Starting Tutorial

Watch the Step by Step Video for More Details

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Kenville Harry

Thursday 2nd of April 2020

ok by Saturday i will let u know and hopefully show u a picture of them as soon as they sprout by the way what fertilizer do you use after 2 weeks of them hatching i usually use stoller harvest more 10-55-10 or miracle grow quick start to give them a quick boost but recently i changed to 20-20-20 any recommendations

dorothy stainbrook

Friday 3rd of April 2020

20-20-20 is fine. I grow on a small farm and only use compost for fertilizer. Peppers don’t need a lot of fertilizer. The 20-20-20 is good in the beginning stages but back off after they start to mature.

Kenville Harry

Sunday 29th of March 2020

hi there i used the pre soaking method with my bell pepper seeds but i left them for 36 hours soaked will they still germinate or should i toss them away ?

dorothy stainbrook

Sunday 29th of March 2020

Well, I’d try them out. Root rot usually only happens after they’ve started to sprout, so they may still be fine. Really though, the only seeds that need soaking are those with really hard shells like Nasturiums etc.


Tuesday 24th of March 2020

This is only my 2d attempt to grow tomatoes. My soil is very clayey and altho, last year the tomatoes grew well the amount of fruit was not the best. Also just learned not to prune so much as more leaves means more fruit .Also, not to plant with corn. Love reading your site. Very interesting and informative. ThanksOh just remembered some tomatoes split or got blossom end rot. (I have a lot to learn);}

dorothy stainbrook

Wednesday 25th of March 2020

Hi Holly...good for you for persevering even when the first attempt was not as successful as you would have liked! It is definitely a learning process, but well worth it in the end. A few comments: clay soil is tough to grow most things in, including tomatoes. The best thing you can do there is to dig a 3 foot by 3 foot hole and mix in as much compost as you can get your hands on before planting in that hole. Tomatoes really need drainage and clay soil doesn’t drain well.

Re pruning: in general, trimming off all the suckers will result in earlier tomatoes but fewer. Leaving the suckers (or most of them will give you more tomatoes, but they won’t be as early. If you leave suckers on, just be sure to trellis the plant somehow so it doesn’t sprawl on the ground and get disease. Re blossom end rot, see this post on that:

Monday 23rd of March 2020

I love this! And think it really makes me want to slow down and grow some food.

dorothy stainbrook

Monday 23rd of March 2020

Wonderful! I hope to do a lot of Q and A videos throughout the year on “How to Grow your Own Food”. If you’re interested check out my youtube channel (and leave any questions or comments here so I can address them!). Here’s my channel link:

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