How to Start Seeds Indoors

The benefits of starting plants from seed cannot be emphasized enough.  When starting seeds indoors, the grower can choose the strongest sprout, have back-up plants in case of failure, provide ideal germinating conditions which can save water, and ultimately transplant to have ideal spacing conditions.  When transplanting to the outdoors, the sprouts have a better chance when completing for real estate with weeds.

More often, you will grow a higher quality plant than what you could get from a nursery — and cheaper, too!  Growing trees from seed will give a true to type plant, whereas buying a sapling from a nursery could be a tree that has been grafted onto a weed’s root system.  If your tree dies, but the roots survive, the roots will spread the weed that the tree was grafted onto.

If you are saving seeds as well, then your seed stock will increase in successful germination rates and be more ideal for your growing conditions!

Supplies You Will Need


Choose non-GMO, heirloom seeds especially if you would like to save your seeds.  I like these seeds. Genetically modified seeds are illegal to save.  Many farmers have lost their livelihood from being sued by Monsanto for cross-contaminated from birds/bees/wind leaving a Monsanto-patented seed in their field (source). Avoid hybrid plants as well as these are sterile.

Paper Towels

Paper towels will keep the seeds moist as they begin to germinate.

Ziploc Bag

Sandwich size Ziploc bags will hold the damp paper towel with the seeds.  Be sure the mark the outside of the bag so you remember which seeds you started.

Seed Cups

These seed cups provide plenty of growing room to prevent disturbing the roots during planting.  The sturdiness allows you to reuse these cups every year making them an economical choice. You could try an alternate method like yogurt cups, but you will need to make sufficient drainage in the bottom.  Egg cartons are too small for root growth.  Toilet paper tubes could work, but will disintegrate after a few waterings.  Likewise, biodegradable seed cups seem like a great idea, but they are not reusable and disintegrate too quickly when watering your sprouts.

Seed Tray

These seed trays complement the seed cups listed above.  The cups nestle in each slot of the tray making it easy to carry and not likely to tip over.  They are sturdy and reusable so you may use them year after a year.  The design makes them drain well and resist mold issues.


Not any soil will do.  Potting soil is too heavy and will pack down too much, and backyard dirt will not only be too heavy, but also could carry microbes that could attack your young plant.  The soil must have the right composition for seeds to get off to a good start.  Stay away from non-organic soil mixes as they may have synthetic fertilizers in them.  Synthetic fertilizers, while they seem to work temporarily, deplete the soils of minerals.  I love FoxFarm’s Seed Starting Soil.

Grow Lights

Since we’re not growing unique or tropical plants, we really don’t need expensive grow lights.  Regular annual garden crops grow excellent under regular fluorescent shop lights making it very affordable to start seeds indoors.


Be sure to check the weather before starting seeds. It is not fun to start some sprouts only to realize that the season is too hot or too cold which they will never survive. The back of the seed packet should give a good idea of the proper time to start seeds indoors.

Prepare the seeds

I like to give the seeds a good soak in warm water. Fill a cup with warm drinkable temperature water (about 105F) and put the seeds in.  Let this cool to room temperature.

Moisten a paper towel with warm water and place the seeds on the paper towel. Fold the paper towel and place in the Ziploc bag.  Wait 3-4 days.  The Ziploc bag will keep the moisture in.

pea taproot
Taproot of a pea

After it has been a few days, check seeds regularly for a taproot. The taproot begins to emerge from the seed first.  After the taproot is visible, then the seed is ready to be planted in the seed cups.

Prepare the cups

In a mixing bowl, add soil and warm water. Make sure it is not too wet, but thoroughly moistened.  Dry soil will absorb moisture from the taproot and the plant will die; therefore, it is important to use damp, but not soggy.  If you squeeze a handful of soil, it should feel wet, but not drip.  If it drips, then it is too wet.

Fill the seed cups with the moistened mix. Press it down so that it is relatively firm.  Don’t leave air pockets, or it will stop the roots from growing.  This is called air-pruning.  Air-pruning is a natural process where the individual root tip dries out and stops growing when it comes into contact with air.

Begin to plant

With the tip of your finger, make an indent in the soil for the seed to be planted.

When taking the seed off the paper towel, be very careful not to let the roots dry out during this process, nor break one of the taproots if it has grown into the paper towel. It’s better to cut around the taproot and plant it with a piece of the paper towel, than to break the taproot.

In nature, seeds lay on the top of the soil, so I like to plant them with just a teeny tiny bit of their seed casing showing. Be sure to plant the seeds with the taproot down!  Otherwise, it may take longer for the sprout to pop up as the taproot tries to find its way down again.

Place the seed cup, with the newly planted seed in the tray.

Water the seed trays

Remember how I warned you not to plant the seed in soggy soil? Well, now we’re going to gently water seed cups to help settle everything. Would have it been fine to plant in soggy soil in the first place? Possibly! But my sensei taught me this way so I stick to it because it works. Take your seed tray to your sink and on very low pressure, gently water the seeds in with bathwater-warm temperature.

Turn on the lights

Now place your seed, ideally under a pair of low-cost fluorescent shop lights, and suspend on chains about 2 to 4 inches above the growing tops of the seedlings. Two bulbs ensures a steady light source.  While we can’t see the flickering lights, it disturbs the plants’ growth.  Two light bulbs ensures that they alternate their flicker.

Turn off the lights

At night, turn the lights off. If you leave the lights on all night long, then when you plant outside, the minute nightfall comes, the plants will think fall has arrived and will go dormant preparing for the winter.

Rotate the trays

Lastly, turn the trays the next day, or rotate the seed cups, so that the plants grow relatively straight and do not grow sideways trying to reach the light.

Water daily and mist regularly so that the soil does not dry out.

When the sprouts emerge, it’s exciting to watch the new growth. I am amazed by it every time.  The first leaves will push off the seed casing; then after a couple more days, the first true leaf will appear.

sprouted plant
True leaves on the sprout

Begin the hardening off process

Once the first true leaf grows, then begin hardening off to plant in the garden. Make sure to check the temperatures and wind outside before hardening off or planting.  With these seed cups being a decent size, the sprouts can hang out for a bit inside until the conditions are right to begin hardening off or planting.


This concludes from start to finish how to successfully start seeds indoors.  It may seem time consuming and a lot of needless steps, but I have had success with this way every single time.  Check out further posts on how to harden off and get your plants in the ground!

Check out our blog post on the biggest mistake farmers make here.

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1 thought on “How to Start Seeds Indoors”

  1. Thank you for posting this! I’ll look forward to reading more! I didn’t do well last year with my indoor starts so I’m excited to have this new information for this year!


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