Indoor Seed Starting

| How-to, Learning

Indoor seed starting gives you a jump on the growing season. If you wintersowed your flats outside, and they’ve had enough time outside, you can simply bring them and start the germination process indoors.  Or, if you stratified your seeds in your fridge via a medium or paper towel method, you can then sow the seeds as you would for any annual or vegetable plants. 


Seeds: Use fresh seeds from a dependable source. You can use older seeds, but sow them more heavily as their germination rates will decrease. For those that need cold-moist stratification, that needs to be done before planting indoors.

Growing flats: You can purchase these, and they come with clear plastic tops and a bottom to hold water. Having a top/lid is important to maintain humidity and warmth. Some people re-use the containers salads come in. Be sure to put holes in the bottom for drainage and have some kind of tray to put underneath to capture water that drains.

Tape and markers: You will need these to identify what you planted. Having the date sown is also helpful.

Seed starting growing medium/soil: There are special mixes for starting seeds. They are often lighter in texture and density to promote quick drainage. They are also sterile, which is important because young seedlings are very susceptible to diseases (particularly dampening off). Finally, they also have no nutrition in them; they are meant only to get the seeds germinated. The first set of leaves are called cotyledons, and contain the young plant’s nutrient needs. When the first true leaves appear, you need to feed the young plants.

Peat moss is a common ingredient, but if you are concerned about the environment, search for mixes that do NOT use peat moss (coir/coconut fiber is a good option). Peatlands are incredible ecosystems, and they need to be destroyed to get peat moss. They are also one of the top ecosystems that store carbon. Destroying them contributes to climate change.

Regular potting soil: You can transplant your young plants into this medium eventually; once they are sturdy enough to handle, and you can grow them on in this soil without having to worry about fertilizing because there will be fertilizer in the potting mix. You can keep them in this until you are ready to plant outside (usually by the end of May)

Balanced fertilizer: After the young plant’s cotyledons begin to wither, you need to begin to apply DILUTED fertilizer (there are often directions for ratio on the box; usually you dilute to a half).

Lights: Lights are important for your plants to be healthy and strong. My set-up at home has lights hanging from an adjustable chain so that as the plants grow, I can move the lights up further. You do want the lights to be fairly close to your plants–about 1-2 away from the top of the plant. There are special full-spectrum fluorescent lights for plants. But, I have used standard fluorescent lights, one warm and one cool tube. Now, there are LED full spectrum plant lights.

Heating mats: These are somewhat optional, but they really do help to increase germination time (a seed could take 2 days to germinate in warmer soil while the same seed might take 5+ days in cooler soil). Some plants (like tomatoes and bell peppers) really need that warmer soil, so if you are growing those types of plants, then the mat is an essential item. I also think it helps with overall health too because the soil will dry out more quickly.

Table just for your seeds: Having a table set aside for your seeds is important. It needs to be impervious to water, or you are okay with water stains on it.

Plastic sheeting: My seed starting set-up is downstairs, and I have cats who like to get in there and graze on my seedlings, so we concocted a sheet wrap that encloses my table. The wrap helps to keep the temperature somewhat moderated (warm when lights and mats are on), and it cools off a little at night. I think it’s important for the health of the plants that they get to mimic the outdoor conditions they will experience. We use velcro to secure the sheets to the table.

Mister/sprayer: Helpful to keep surface sown seeds moist without drenching the bottom layers of the soil.

Small fan: Once the seedlings begin to appear, having a small fan to help with air circulation is very helpful. The air movement should be barely noticeable.

Timer: You can use a timer for your lights and heating mat. Lights should be on for 12-14 hours per day.


  • Pre-moisten the soil in a separate bowl before putting it into the growing containers. The seed starting material takes a few minutes to saturate (these mixes are hydrophobic to avoid saturated soil, enemy to young seedlings.
  • Fill container with soil; you might want to leave about ½ from the top depending on the size of your seeds.
  • Sow seeds. I usually put more in the sections than will grow there long term. You can thin out seeds (called pricking), or let them grow and thin and repot out later. That is something that takes a little trial-and-error.
  • Depth of planting: Follow the packet’s directions. Seeds that are surface sown need careful attention that the growing medium does not dry out at all. Sometimes I will sprinkle a tiny amount of soil on top (not enough to cover all of the seeds at all) to help with moisture. These often need light to germinate. As soon as they germinate, mist them daily.
  • Be sure cover is over the container.
  • Check on your seedlings daily. Once they pop up, you will probably want to check on them at least 2x/day.
    It is important to observe things really well.
  • Once the seedlings begin to germinate, check moisture daily. You do not want things too wet or too dry.
  • You can water from the bottom. Put some water in the bottom, about a ½” at first, and the soil will wick it up. Do not put so much in that you have standing water all day long. That means the soil will be saturated for a couple of days, and that is a recipe for all kinds of problems.
  • As they get taller, start to lift gradually the cover. Sometimes I put a little piece of paper to lift the edge of the lid so that the plants acclimate to a less controlled environment. Eventually, they will be too tall for the lid. One of the basic rules of thumb is to do things on a gradual basis.
  • Once the lid/cover is off and they have 2-3 sets of new leaves, and you are not using a fan for circulation, it’s important that you help them strengthen their stems by gently running your hand over them.
  • If you grew your seeds in a sterile seed starting mix and there is no fertilizer, you now need to add a DILUTED fertilizer.
  • Once they are robust and easy to handle, you can transplant them into a potting soil mix that does have fertilizer. Then you won’t need to worry about fertilizing any longer.
  • As they get taller, adjust the lights to keep them just above the plants but not touching the bulbs.
  • I rotate the flats on a daily basis because so that all plants are getting the light they need. If you see plants on the outer edges leaning, they are not getting enough light. Rotate so that they are directly under the lights.

Most of the problems that can happen are the result of too much moisture and not enough air circulation.

One of the most common problems is dampening-off which is a fungal disease that causes the seedling to wither away at the point just above the soil line. Remove any affected plants-throw them away–wash your hands, etc before handling anything else. The fan will be a very important tool to use. Let the soil dry out a bit.

Fungus gnats can also be a problem; they can be in your potting soil. Their larvae eat the roots of the seedlings. Allowing the soil to dry out a bit will also desiccate the larvae. There are traps you can get for these pests.

I am always happy to see spiders in my set-up as they will help with controlling these pests.

Checklist for each stage:

Freshly sown seeds:

  • Check that lights/heat matches the needs of your seeds
  • Check that the soil stays evenly moist.
  • Check daily and watch for signs of sprouting.

Young sprouts/cotyledon leaves:

  • Check that lights/heat matches the needs of your seedlings.
  • Lift a corner of the cover so that air begins to circulate and excess heat and moisture can escape.
  • Regular fluorescent tubes should be just above the sprouts.
  • Check that the soil stays evenly moist. Not too wet and not too dry.
  • First true leaves/seedlings:
  • Cover should now be completely off.
  • Diluted balanced fertilizer (follow directions of the manufacturer; usually half-strength)
  • Do not fertilizer everyday–apply once a week. As with water, not too much and not little. Fertilizer can build up, can kill your seedlings. If they get pale, then they need some food. I would almost err on the side of less fertilizer.
  • Lights should be just above the seedlings.
  • Begin gentle air circulation or rubbing hands over your seedlings to strengthen stems.
  • If anyone is leaning, they are not getting enough light, rotate them around or consider adding another section of lights.
  • Check for signs of disease or pests.

Robust seedlings/multiple pairs of true leaves:

  • You can now transplant these into a potting soil and/or larger pots/containers as needed if you want, or continue with diluted fertilizer. Once in regular potting soil, you can stop fertilizing.
  • Maintain watering; you might need to do more watering now as they get larger.
  • Keep lights above them; you might need to raise the lights every other day as they will now be growing at a faster pace. Observe for signs of disease and pests.
  • As you get closer to planting outdoors, start the process of hardening off.” Your seedlings will need to get tougher gradually and get used to their new home. 🙂 I often set out my trays somewhere fairly protected where they will only receive indirect light (as in under a table) for an hour or two the first day. If they were ok with that, you can extend the time every day. You might try letting them get gradually more sun if they are to be grown in full sun conditions. Perhaps let them get a little evening sun or morning sun for a half-hour. Do not set them out on a very windy day for their first outdoor venture either. Check the soil moisture–with the increased air circulation and sun, they will dry out faster.
  • Once it’s going well, start to leave them out overnight on warm nights, so they get used to night temps and conditions.
  • Once we are out of danger of frost, you can transplant your seedlings into their permanent homes. Transplanting is pretty stressful, so they will need some more coddling for the next couple of days. Even if they are a full sun plant, they will need some protection from full sun while they are getting their roots all sorted out. I place a turned over container (with holes) or set up some kind of shading situation (might take some sticks to form a teepee and then place some pruned branches over it).
  • Water every day.
  • Enjoy the products of your nurturing!

Rules of Thumb for a Green Thumb:
1.Goldilocks principle–not too much, not too little.
2.Do everything gradually.
3.Observe carefully.