The Complete Guide to Indoor Seed Starting

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This is the complete guide to indoor seed starting. We will learn why you should start most of your seeds indoors and how to do it to increase production and simplify your garden.


Starting seeds indoors at the end of winter, when you are about to lose your mind, is a fine method of therapy. It saved me (or rather my kids…) more than a few times.

When thinking about seed starting, most people immediately think about late winter, about getting ready for the growing season and for spring planting.

But you can use the many advantages of indoor seed starting not only during those late winter days but all through the summer and early fall as well. It gives you so much more control over the fragile, young seedlings. 

The Complete Guide to Indoor Seed Starting…

This is the complete guide to indoor seed starting. From beginning to end, everything that you need to know about how to start seeds indoors.

Here is what we are going to go over in this guide…

  1. Benefits of indoor seed starting.
  2. Which seeds can I start indoors?
  3. When should I start seeds indoors?
  4. Seed starting equipment.
  5. How to start seeds indoors.
  6. What happens next.

Benefits of Indoor Seed Starting

First things first. Why would you even want to bother with starting seeds indoors? Well, here are a few of the benefits…

Early harvest –  this is the first benefit that comes to mind, right? If you put out larger, established plants into the ground instead of seeds when the weather is finally warm and the soil can be worked, you’ll get to harvest vegetables from your plants much sooner.

Stronger plants –  seedlings are such a delicate thing! They are just like babies, really. You have to protect them, nurture them, feed them, sing to them… When they are closer to you, inside the house, this is much easier to do.

Strong winds, cold nights, strong sun, extreme changes in temperatures, heavy rains… They all increase your chance of losing those babies if they are out in the garden when mother nature is not so steady at the beginning of the season or too extreme later in the summer.

If you take care of your seedlings right and nurture them to a strong little plant, two things will happen. First, by the time they are ready to go outside the weather is a bit calmer and might be more predictable. And second, they’ll be stronger and much more ready to hold their own against mother nature.

Better control of spacing – when you plant an actual plant, it’s much easier to measure correct spacing than if you planted seeds in the soil. You won’t have to thin seedlings and you reduce the chance of bare patches due to seeds that didn’t germinate or seedlings that were damaged or consumed by vicious bugs.

Away from pests – this past spring, I planted carrots four times. They germinated beautifully and quickly reached about an inch in height. Then the next time I went to check on them they were gone. Nothing was there! This happened all four times, I planted hundreds of seeds and I only had two carrots reach harvest size. Two. How pathetic is that?

Thing was, I couldn’t see any pests. It could have been birds or God knows what… 

Now, carrots are not the kind of seeds you’d start indoors (more on that soon), but the point is, birds and pests love young plants. They are so tender and tiny, so defenseless and easy to consume. Keeping your seedlings indoors will keep them away from those lurking pests.

Greater variety – if you go shopping at the local garden center in early spring, you’ll notice maybe two or three varieties of tomatoes and mostly one variety of everything else. But there are so many other interesting varieties to choose from.

When you start your own seeds you can choose from a greater selection.

Now, a word of caution here… It’s super easy to get carried away while browsing through those seed catalogs while the snow is falling outside your window. You know that’s true if you ever opened a seed catalog in January…

I encourage you to choose one or two main varieties that are known to do good in your area and maybe another experimental variety for you to try. Don’t go order seven exotic varieties of tomatoes and none of the main crop varieties because you might end up with very little to show for your hard work.

Cost saving – a seedling from the local garden store will cost approximately the same as a pack of 50 or more seeds. Of course, you should calculate the soil you’ll use, the containers, electricity, fertilizer, and so on… But overall I think you’ll save some money if you start your seeds yourself.

Fun – plain and simple, starting seeds indoors is just fun! It’s a great activity to do with the kids, you get your gardening fix when it’s still very cold outside, it might help you carry on through those last few weeks of winter, and it’s so satisfying to see tiny seeds turn into beautiful, strong plants that feed you and know you’ve done it yourself!

Which Seeds Can I Start Indoors?

Holding seeds.

Jean-Martin Fortier, in his book the market gardener (really amazing book!), writes:

“Given the choice between transplanting a crop and direct seeding it, we always prefer to transplant. The advantages of this method are worth all the effort and expense, especially if intensifying production on a small plot is the goal. The success of our growing operation therefor depends on our ability to start seeds indoors.”

I think that this is pretty much what you’d hear from most professional growers. If it can be started indoors, it will be.

It’s actually much easier to list the vegetables you won’t start indoors. You can grow all of these in larger containers if you’d like, however, they generally don’t like being transplanted:

Beans (although I saw someone start those in toilet paper rolls and transplant them with the roll but I’ve never tried it), carrots, corn (some small scale farmers do start corn indoors, usually for the home gardener it’s not common to start corn indoors), mesclun mix, peas (possible to start indoors but not common), radishes, turnips, potatoes, sweet potatoes (you’ll start these from slips).

Aside from these vegetables above, you can start all seeds indoors.

When Should I Start Seeds Indoors?

To find specific dates for starting seeds indoors in your area you can use a really great page on the Johnny’s Selected Seed website. You can go HERE and enter your last frost date (you can find this date by Googling “last frost date for *enter your zip code*), and the table will give you the dates to start your seeds indoors for spring and summer transplanting for each plant you’ll be growing.

But while you’ll read about starting seeds indoors at the end of winter for spring and summer transplanting typically, I tell you, you can take advantage of starting seeds indoors all through the growing season, especially if you are interested in growing a fall garden or if you have a small growing space.

Let me give you an example…

Here in central NC (growing zone 7b), soil temperature is very high in September after a hot and humid summer. First freeze date is November 15th. There are many crops, for example, cabbage, that take more than a couple of months to mature.

So if I plant my cabbage seeds when it starts to cool down in the middle of September they most likely won’t reach maturity by the first freeze, but if I plant them earlier, in the hot soil, they won’t germinate.

What I can do to solve this problem is plant my cabbage indoors where the A/C unit keeps the temperatures nice and cool. I’ll plant it at the beginning of August or even at the end of July, and by mid-September when the outside temperature and soil temperature is much more comfortable for cabbage it will already be a few weeks old and will be able to reach harvest size by the first frost date.

What I am trying to say, is that most of the time people think about starting seeds inside because it’s too cold outside, but think about starting seeds indoors also because it’s too hot outside.

Another reason to start seeds indoors during the season is space. Let’s say I have potatoes growing in my garden.  It will be mid to late June before I can harvest them. Let’s say I want to plant cucumbers in their place. Instead of waiting until it’s harvest time and then plant seeds of cucumbers where I harvested the potatoes, I can start the cucumbers indoors at the beginning of June and by the time I am done with the potatoes I have established cucumbers to plant.

See how this works? Really, if you wanted to, you could make your seed starting set-up work for you all season long, to help heat, cool, and maximize production for the space you have.

Seed Starting Equipment…

It will take a little bit of work to gather your equipment and materials, but as I said before, once you put this together you can use it all through the season and for years to come.

Seed starting shelves.

Seed starting shelving unit – all this is is a shelving unit with cool fluorescent shop lights. Read more about my grow light system here: Simple DIY Grow Light Stand For Indoor Seed Starting. 

Find a spot in your house that is out of everyone’s way. It can be a corner here or there or a basement, for example. What you need to remember is that you need to be able to control the temperature in the room where the shelving unit is, so a cold or too hot garage or shed probably won’t do.

Find or buy a four-foot wide shelving unit and for each shelf install one or two cool florescent shop lights depending on how deep the shelf is.

Make sure to use the chains that come with the shop lights so you can change the height of the lights as the plants grow (more about that later).

Seed trays, blocks or pots – I like to keep it simple and use seed trays. I buy the leak proof trays. In them, I place plug flats or pots depending on the plants I am growing. There are other options as well…

You can use soil blocks (a mold that makes blocks of soil in which you can grow your seed and then transplant into the garden, you can read more about this technique here), or toilet papers rolls, or just pots (biodegradable or not).

Whatever you choose, make sure you remember that you are not going to keep the plants in there forever, just a few short weeks… And, seed starting soil isn’t cheap so you want to maximize production per flat.

Also, I save the trays and flats and reuse them for a few years before buying new ones. You can sanitize them before using them again to prevent disease. To do that, at the end of the season, make a solution of one part bleach to nine parts water and wash your trays. Make sure they dry completely before stacking them and storing them.

Seed starting soil – if you choose to use soil blocks, you will have to make your own soil block mixture. Honestly, this is the reason I go with the good ol’ trays and flats. There are many recipes online for seed starting soil for soil blocks but it was just too time-consuming for me to gather all the ingredients.

So I keep it simple with organic seed starting soil that I purchase from a local nursery and worm castings that I order from Amazon. If you can’t find seed starting soil locally you might need to order it online.

Since I grow organically, it’s important to me to start with organic seed starting soil because I don’t want the chemical fertilizer that is in the other soils. I add the worm castings to make sure the little seedlings have plenty of food. It will really make a difference in your plants (we’ll go over how to mix it below).

A large bowl – since we are going to take a moment to mix our soil with worm castings, make sure to have a large mixing bowl or a bucket on hand for this job.

Tags – I always, always make the mistake of thinking I’ll remember what I planted when. It might be easy to recognize a tomato seedling from a cucumber one, but you are not going to remember when you planted them, especially if you plant a few trays. And will you be able to recognize one variety of tomato seedlings from the others?

I use little plastic tabs and a Sharpie. I write what I planted, what variety it is and the date it was planted. When I transplant the seedlings to the garden I stick the tag next to them too. It’s great to have the date in front of you all the time so you can learn how long it took the plant to be ready for transplanting, how long it took it to flower, and how long it took from planting to harvest, and so on.

And, of course, you want to have the variety name so you can learn which variety was more successful and tasted better.

It is on my calendar to go over my seed starting equipment the first week of January. This gives me enough time to order supplies or purchase whatever I need locally before it’s time to start planting.

How to Start Seeds Indoors…

Alright, I think we are ready for planting! I am going to assume that you have your shelves and grow lights ready and installed and that you gathered the rest of your supplies. Let’s break the process of planting down into a few simple steps.

Step 1: Prepare The Seed Starting Soil…

Mixing seed starting soil.

I use a big mixing bowl to mix the soil and worm castings. I wish I had an exact recipe here for you but I don’t. I just fill the bowl with organic seed starting soil and add about a cup or so of worm castings. You don’t need a lot of the castings, they are very concentrated.

If I had to put it in measurements, I’d say 10 parts soil to 1 part castings or something along those lines.

Seed starting soil ready for planting.

Mix the castings well with the soil and then add some water to moist the soil so it packs better into the flat’s cells.

Step 2: Prepare the Flat and Tray…

Leakproof seed tray.

This, in the picture above, is the leak-proof tray. It makes it easier to water the seedlings and it saves a lot of mess on the shelves.

Filling the flat with seed starting soil.

Inside the tray, you’ll place your flat or pots. You can find flats that have 38, 50, 72, 128, and 200 cells (there might be a few more options).

So which one should you use? This will depend on what you are planting and how long you plan on it staying in the flat. I like to keep it simple, so I use 128 cell flats for lettuce, chard, spinach, basil and so on… Crops that are not too big and don’t need to spend too much time in the flat.

For larger plants, I use the 72 or 50 cell flats or sometimes 4”x4” pots (for tomatoes, for example). Those will be crops like watermelon, pumpkin, cucumbers…

You are going to have to read about each seed you’re going to start or just experiment a little bit. You can also feel free to ask in the comments below and we can all share our experience and help each other.

Once you choose your flat, fill it with soil…

Seed starting flat filled with soil.

This is the reason a lot of large operations use the plastic trays, it’s very simple to fill them with soil. You simply dump some soil on top and smooth it with your hand all over the flat…

Removing large pieces of wood from the seed starting soil.

Make sure to get rid of little pieces of wood if you find any.

Pressing soil into the cells of the flat.

Once your flat is filled with soil, use your finger to press the soil into the cells, if there is not enough soil in one of the cells, this is the time to add more. This will also make a little hole where you will plant your seed.

Step 3: Plant Your Seeds…

Seed starting flat ready for the seeds.

Once your tray is ready, it’s time to plant your seeds…

Planting a couple of seeds in each cell.

Remember to check the packet of seeds for the right depth of planting. Place one or two seeds in each cell. If your seeds are old, definitely plant two seeds in each cell. Some people choose to place a couple of seeds in each cell anyway and thin to one plant in a cell later.

Covering the seeds with more soil.

Once the seeds are in place, dump soil on top of them and smooth it over the whole flat covering the seeds.

Seed starting flat is ready for the grow light shelves.

The last thing you have to do is water your flat. Be gentle here, you want to gently shower or even mist the flat so you don’t move the soil and seeds from their cells.

Step 4: Place Your Flat on the Growing Shelves…

Now your flat is ready to go inside. At this stage, you don’t really need to turn on the light. You can place the flat under the shop light but leave it off until the seeds germinate.

Seed starting flat on the shelf.

The thing is, once the seeds germinate, when you just see them starting to poke through the soil, the light has to come on immediately. I don’t have my growing shelves inside my house, they are in a room that we have on the farm across the road so I prefer to turn the light on when I place the flats on the shelves.

Here are a couple of frequently asked questions…

Do I need a dome (a clear plastic cover for the flat)? I think it’s optional. I don’t use them but I also have a very controlled environment for germination since we start seeds in a separate room where I can control the temperature and moisture.

A dome will create a perfect environment for germination by keeping the soil moist and warm. So depending on where your growing station is placed, you might decide to use one but again, it’s optional.

Do I need to use heat mats? Heat mats warm the soil and help seeds germinate fast. I say if your room holds a 70F or so (basic room temperature) you are good with most seeds. It might take them a tiny bit longer to germinate than if you had a seed mat (like a day or two longer), but in my opinion, it’s not a big deal.

Summer crops like cucumbers, pumpkins, and tomatoes will probably love a heat mat, but again, I germinate them just fine without one, it’s one less thing to buy and store and I am all for that.

Step 5: Control Growing Conditions…

Here are the best growing conditions for indoor seed starting… Try to set your space to provide those conditions as best as you can.

Air temperature – for the germination stage, try to keep the room temperature around 70 degrees F or so for all seeds. The difference in temperature comes after the seeds germinate.

Crops are divided into two groups: cold weather and hot weather. Cold weather will be vegetables like lettuce, chard, spinach, green onions, and so on (things that grow early in the spring or in the fall garden). Hot weather crops are all the summer stuff like tomatoes, cucumbers, melons, pumpkins, and so on.

When it comes to room temperature, the cold weather crops will grow best at 65 -70 degrees F. Hot weather crops will grow best in the upper 70s or even 80 degrees F. Once the seeds in your flat germinate, it’s ideal to adjust the temperature depending on what you planted.

But what if I have both cold weather and hot weather crops on my growing shelves at the same time, you are asking?

Well then, keep your air temperature at around 70 degrees F and once the cold weather crops go outside (which will be before the summer crops) bump the temperature up a bit (if your growing shelves are in a certain room in the house, you don’t have to heat the whole place, you can use a small electric eater in the room where the growing shelves are).

Air circulation – to prevent disease and mold, it’s important to maintain the movement of air around the seeds. This is easy to do. Just place a small fan in the room. You don’t have to keep it on all the time. But a couple of times a day for 10 or 15 minutes each time will do just fine.

Light – all this will not work without light. Period.

Use cool shop lights around your plants so you don’t cook them, and keep the light 2” from the plants at all times. You will need to adjust the height of the light as the plants grow. This is easy to do if you make sure you use the chain that comes with the shop lights when you install them.

You want to keep the light on for at least 8 hours, 12 is better. For example, turn it on at 8 am and off at 8 pm. Using a timer for this is a great time-saver.

Moisture – most plants (when we talk about vegetables, fruits, and flowers) don’t grow too well if the air is too dry. To add some moisture, you can use a humidifier or, if you only have hot weather crops growing and the temperature is high in the room, just place a dish with water somewhere and it will evaporate and add water to the air.

Another option is to keep a small spray bottle with water close by and spray the plants a couple of times a day.

Step 6: Caring For the Seedlings…

I know you must be thinking, oh boy, this is a lot of work… and you are right, starting seeds indoors is a lot of work, but watching seeds germinate and little plants grow into big and strong ones is so much fun (and once you’ve done it a couple of times it’s really not that hard).

Here is how to care for your plants…

Water – the babies gotta drink. They are so so so fragile, so be careful when you water them, a gentle shower or mist every other day will do but my favorite way of watering is adding half an inch of water to the leakproof tray. Very quickly, the little plants send roots that reach the water and they can drink whenever they want.

Little seedlings in a seed flat.

Thinning – if you planted more than one seed in a cell and more than one seed germinated you will have to thin your seedlings. Wait a couple of weeks after the seeds germinate to see which one looks better. Then use clippers or scissors to cut the other one, the weaker one, at the soil level.

Don’t pull because it might damage the roots of the remaining seedling.

Fertilizing – remember that we mixed the soil with worm castings. There is really nothing better than worm castings when it comes to organic fertilizing if you ask me. I usually don’t fertilize anymore but if you feel that your plants can benefit from a little bit more worm castings you can add it on top of the soil anytime and water overhead (to wash the nutrients into the soil).

Re-pot – some of your plants might need to be re-potted. What that means is that it might not be the right time to transplant them out yet but the container they live in indoors is getting too tight for them.

If you leave them in that container they’ll start to struggle (you might notice that they start yellowing or that the soil dries too fast after watering) so you’ll have to move them to a bigger container.

Some plants benefit from re-potting. For example tomatoes. The reason is that the stem of the tomato can grow roots, and so when you re-pot, you sink the plant lower into a pot of fresh soil (basically bury the plant all the way to the first leaves) so the stem (that is now covered with soil) will start growing roots. More roots = stronger plants.

Honestly, I try to avoid re-potting (just because I don’t like doing it…). With most of my plants, once they grow in the cell or container they are in, they go to the garden. I might even start the seeds a week or so after the suggested date so that I have a better chance of the weather being good for transplanting when the plants are ready.

With tomatoes, I start them in a 4”x4” container. I fill the container with an inch of soil mix and plant the seed. The seed germinates, I let it grow for three or so weeks. Then I add soil around the stem (using a spoon and being very careful not to break the stem). I’ll let seedling grow for another three weeks and then fill the rest of the pot with soil. Two or three weeks after that the tomato plant is ready for transplanting.

What Happens Next…

Seeds are ready for transplanting.

After growing the plants indoors for a few weeks, the seedlings are not so small anymore, the weather outside is warm enough or cool enough and it’s almost time to transplant your plants to the garden.

But your plants are not used to the sun, they are not strong enough to hold themselves in the wind, and rain might break them. After all, they were growing in this perfect environment up until now.

So from here, your next step is to harden them, or in other words, get them gradually used to the weather outside and then transplant them to the garden.

I cover all of this information in my post about how to transplant seedlings.

A few more helpful posts:

  1. How to Plan a Vegetable Garden in 7 Easy Steps.
  2. How to Create a Planting Schedule for a Vegetable Garden.
  3. Best Varieties to Grow in a Kid-Friendly Vegetable Garden.
  4. How to Start a Raised Garden Over Grass.
  5. Easy Garden Preparation, the No-Till Way.

OK look, starting seeds indoors is like running a marathon, I imagine. You finish it thinking I am never doing this sh***t again! Your muscles are sore, you are tired, sweaty, stinky, hurt…

But then before you know it you want to do it again. You have to, you miss the pain, you miss the recognition, you need to feel the feeling of achievement.

This is all coming from my head, you know. I have never and probably never will run a marathon…

But I did start 600 seeds this spring and let me tell you, it was painful. Planting, caring for, taking the trays in and out to harden every day… And the transplanting! 600 transplants by hand! Good Lord. I thought my body was about to break.

But now my plants are in the ground and growing beautifully, the cucumbers are almost ready for harvest, little green tomatoes are peeking at me from between the leaves. The basil is as green as Mr. Hulk, the peppers and eggplants are getting more and more beautiful every day…

And to know that I started all these beautiful and strong plants from a tiny seed in a tiny cell inside my house… It’s definitely a sense of accomplishment!

I hope that this post gave you enough information to go and do this yourself. It might be a good amount to figure out the first time, but I’m a 100% sure that you’re going to be hooked for life after that!

Garden Workbook Cover

The Garden Workbook is Here!

In part one of this book, we’ll go over how to set up and grow your best garden yet.

Part two consists of 16 garden printables to help you plan, record, and manage your garden properly!

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4 thoughts on “The Complete Guide to Indoor Seed Starting”

  1. I’ve grown a Hobby garden for years, but this will be my first time to start seeds indoors. I got a lot of useful information from your post. Thanks!!!

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