Start Your Seeds Indoors


Are you ready to give growing plants from seeds a try? Starting flowers and vegetables from seeds can be fun, sometimes challenging, and very rewarding. Remember to keep it fun and enjoy the fruits of your extra work.

Why Grow from Seed?

There is nothing like watching young plants change on a daily basis. It’s amazing, actually, how fast tomatoes reach for the sky. Knowing that your efforts have ensured that a tiny seed has reached its full potential is one of the most rewarding things we can do as gardeners. I always do a little celebratory dance when I see my first seeds sprout from the soil.

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Another reason to grow plants from seed is that you have found a particular variety of flower or vegetable that you want to try. If you frequent your local garden centers, which of course you should do habitually, you have an idea which varieties they offer from year to year. I know that I can always get Sweet Million cherry tomatoes, for example, but Sun Golds go so quickly I can rarely find them. Instead, I grow my Sun Golds from seed. I also grow several varieties of peppers and tomatoes that I can’t purchase from a garden center near me. They just don’t offer them.

Is it your time to experiment? Have you been successful with what you’ve grown so far, be it houseplants or flowers in the garden bed? Consider taking that next step and starting a few plants from seed. Don’t go too crazy when you first start out because it can get overwhelming if you get too ambitious. Gardening often infects you in stages and starting plants from seed may be your next logical step.

Growing from seed can also be a lower cost. At least that’s what you would think. After buying supplies, soil, grow lights, shelves, fertilizers, and the like, you aren’t going to be ahead of the game. So grow from seeds because you like it, not because you want to save money. It doesn’t pencil out for many years.

Getting Seeds Off to a Good Start

The overall goal when you are starting seeds is to replicate, as close as you can, the optimal germinating and growing conditions for whatever plant you want to grow. This means considering air temperature, soil temperature, humidity, and light intensity. So start gathering your supplies and let’s get growing.

First, let’s find a room in your house that tends to be on the warm side. This will get your plants growing the fastest. Don’t overly worry about this, though. I’ve been growing seedlings in my utility room because it is the most convenient place. The temperature hangs around 60-65 degrees. Not the most ideal temperature, but it does work.

Next, soil temperature is most important during germination, that period after you plant the seed until it emerges from the soil. Many seeds, like tomatoes and peppers, will need a seed heating mat.

Seed Heating Mat
A seed heating mat, like this well-used one of mine, is a good investment if you are starting seeds such as peppers and tomatoes.

These mats raise the temperature only slightly, but make a big difference in how fast your seeds will sprout. You won’t need this mat for things like broccoli or cabbage, but for those seeds that need warmth to wake up and grow, you can easily cut the germination time in half.

These mats are also waterproof so if you spill things on it you aren’t going to be in trouble. For this reason, it is not advised to improvise. These heating mats are inexpensive and will last for years to come (click here to buy one from Amazon). Don’t scrimp on this item.

Next let’s look at soil and containers. While I generally use regular potting soil amended with vermiculite and perlite to start my seeds, I’d advise using seed starting mix. The bag will specifically say it is for starting seeds and the soil is much lighter in texture and has better drainage than regular potting soil. Buying this soil in smaller quantities just makes your life easier when you are getting started. There are a variety of seed starting mixes on the market. It is always easiest to purchase a soil mix that is made to start seeds. (Click here for an example of a seed starting mix on Amazon)

What containers you will use is always going to depend on what’s available to you. If you are big on recycling, you may have a collection of plastic food containers you’ll want to use. Many people have used covered lettuce containers to start their seeds. They work great.

I’m also a big recycler but I have neighbors who have brought me many three to four inch square pots that petunias come in from the nursery. One year, my neighbor went crazy planting ornamentals around her yard and she brought me a bunch of them. I like them because they are all the same size and fit perfectly in the inexpensive trays. If I buy plants, I will generally buy them in this size pot, click here to see them on Amazon. I haven’t actually bought containers for seed starting in many years.

Small pots for starting seeds.
I’ve used these size pots for years and they fit perfectly in the trays. The square shape is easier to fit in the trays than round ones.

The three to four inch pots will also grow your seedlings to about the right size. When planting time arrives, seedlings will have just about outgrown these small pots. Every now and then I’ll have to repot my tomatoes, but I’ve learned to just start them a little later and I can avoid this. I’ve never had to repot my peppers because they tend to grow more slowly.

A waterproof tray will be necessary for the pots to sit in because you’ll want to water everything from the bottom. And, of course, you don’t want water to drain all over the floor. (Click here to see a set on Amazon)

A humidity dome is optional. I use them consistently when my seedlings are young and then remove them once they have one set of true leaves. The higher humidity that the dome provides is really helpful to the young seedlings so you may want to consider adding this inexpensive item to your list of supplies.

Planting tray with humidity dome
A humidity dome provides a better environment for seeds to germinate, it perfectly over the tray, it was easier to photograph with it an angle. (Click the photo for more info)

A tray with drainage holes (click here to see one on Amazon) is also optional. I’ve gone to using this tray to start my seeds and then I carefully transplant the tiny seedlings to my four inch pots after germination. In this way, I minimize the number of empty pots because I’m only transplanting seeds that have actually germinated. Any packet of seeds will have 5-10% that won’t germinate. Some seed packets will tell you what the germination rate is so you can plan on starting more seeds. For example, if you want four plants and the germination rate is 75%, you’ll know that you’ll have to plant at least five seeds, but six is even better.

Tomato seedlings
I prefer to start my some of my seedlings in a tray and then transplant them into individual pots when they are still tiny.

The last thing you will need is grow lights and a timer. Can you use a sunny window? Sure you can. But your results won’t be as good as if you use grow lights.

Grow Lights
I have several different kind of grow lights that I’ve accumulated over the years. These are my LED lights. When you shop for them, be sure to look for lights that are specifically for growing plants to get the correct spectrum of light that the plants need to thrive. (Click the photo for more info).

When you use grow lights, you control the intensity and the duration of the light. When are we starting our seeds? Usually during the shortest days of the year. If you use a sunny window, your plants are going to be growing for less hours every day and the intensity will not be enough. You’ll end up with tall, weak plants that are bending toward the window. This is not ideal.

Using artificial lights that are specifically designed for growing plants, you’ll be able to place them within inches of your seedlings. You’ll also be able to have them on for twelve to fourteen hours a day, which signal plants to grow. Both of these things will give your seedlings the best chance to be strong when it’s time to transplant into the garden.

Unless you have decent shelving that you can repurpose for starting seeds, you should consider buying separate shelves. My shelves are placed at different heights to accommodate different stages of growth. A short shelf allows me to hang lights closer to smaller plants. A taller shelf allows more room as the plants grow. If you’re starting small, the top of a dresser may work. You’ll just want to protect the surface from water leaking on it, and have a way to adjust the height of the grow lights.

Other optional items you may want to add later are either a cold frame or greenhouse. Depending on your weather, you probably won’t want to start your seeds in a greenhouse, but you’ll want a protected place where your seedlings can benefit from natural light.

I place my seedlings in the cold frame as soon as possible. For me that means April. The days are getting longer by then and the sun gives them a boost that the artificial lights just can’t duplicate. The sun hitting the cold frame also warms up the inside environment, with the temperature getting much closer to ideal growing conditions ( a remote thermometer is essential for monitoring the inside temperature). With the lid closed, the humidity level also rises which improves the growing conditions, thus increasing the rate of growth.

Sow Your Seeds

Now that you’ve gathered your supplies, chosen your location, and planned for when your plants grow tall, let’s get them planted. As I stated above, I’ve gone to planting my tomatoes and peppers in a tray and transplant them to small four inch pots once they’ve germinated. Other seeds I’ll place in the pots directly, such as cabbage, broccoli, onions, and leeks. Which container to start your seeds is truly a matter of preference.

I have a deep tray in my potting bench that I use for pre-moistening potting soil. You may have a bucket that will allow you to do the same thing. You will be surprised how much water potting soil will hold. Pour in some water, mix it thoroughly, and then add more water if needed. When you hold a handful of the soil, it should not be dripping wet, but instead be evenly moist.

For each pot, overfill it with moist soil and then tamp it down with the bottom of another pot. This gives you a level planting surface.

Filling pots to start seeds
Start by overfilling the pot with moistened soil.
Preparing pots for seed starting
Use the bottom of another pot to gently tamp down the soil being sure to tamp down into the corners.
Prepared pot for seed starting
The result will be a reasonably level soil surface that is ready for seeds or for transplanting seedlings.

Handle the seeds carefully and place one to two seeds into each pot for most seeds. For onions, you may want to plant about a dozen per pot. Then sprinkle moist soil over the top of the seeds. The general rule is to cover the seeds to a depth of the size of the seeds. Depending on what you’re growing, that won’t be very deep. The main thing to remember is that you don’t need a lot of soil to cover the seeds but you do want them covered so that they aren’t sitting on the surface.

You can start a lot of seeds in one pot if you are growing anything in the onion family such as these leeks. They are easy to separate if you use a bucket of water to gently wash away the soil before planting. Using smaller pots than shown also makes it easier to grow the number you want. It’s easy to get carried away!

Once you sprinkle enough soil on top, take the bottom of another pot and tamp down the soil again. This will provide good contact between the seeds and the soil, which is the goal.

Place a label in the pot so you know which seeds you planted, and place the pot in your drainage tray. The other reason I like my square pots as shown in the photos, is because they all fit perfectly in my trays. If you have a humidity dome for your tray, place it on top of the tray and then place the tray on your seedling warming mat (if you are growing seeds that need warmth to help them germinate). Turn the lights on with your timer set to twelve to fourteen hours of light per day, and check the seeds daily.

Pots in tray with humidity dome
Although this is not my photo, this is exactly my preferred set up for pots, trays, and humidity dome.
Plant Labels
Planting labels are easily found. Be sure to use a permanent marker if you are going to place the label outside. You will be surprised how fast the sun will fade the normal ink and leave you wondering which variety you planted! (Click the photo for more info.)

The humidity dome will help minimize evaporation and you may not have to water at all until the seeds sprout. The critical thing at this point is that the soil stays moist. If it goes through a dry period, your seeds will either be delayed in sprouting or won’t sprout at all. If needed, add water to the base of the tray to allow the water to soak the soil from below. Never fill the tray more than about a half inch, the water will be drawn into the soil through the holes in the pots. If you need to water from the top because the top layer just looks too dry, use a spray bottle set to “mist.” This method will not disturb the seeds as they are starting to sprout.

Most seeds will sprout in seven to ten days. Others take longer. The seed packet should say how long it will take for them to germinate. Don’t panic if it takes a few days longer, but the germination period listed on the seed packet should be fairly accurate.

Seeds emerging from the soil
The first leaves to show are the seed leaves or cotyledons.

The first sprout you’ll see are the cotyledons, sometimes called the seed leaves. These are not shaped like the leaves of the mature plant. Sometimes they are shaped like the seed itself. The next leaves that show up are true leaves and small versions of how you would expect the leaves to be shaped. At this point in the seedlings life, they are extremely easy to kill.

It is very important at this point that you maintain the moisture level in the soil. I will keep a little bit of water in the bottom of the tray just to be sure. At this point, the roots haven’t made it to the bottom of the pot and there is little danger of drowning the roots with too much water. The humidity dome, if you are using one, is helpful at this stage and should have the vents open to allow some ventilation.

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As the seedlings grow taller, you’ll have to remove the humidity dome. Continue to water from the bottom if the soil is feeling rather dry to the touch. If you check the moisture level daily, you won’t be at risk for drying out the seedlings and killing them. At no point should the leaves on your seedlings look wilted. At this early stage, the seedlings may not be able to recover from the stress of wilted leaves. Be watchful, because different pots may need water sooner than others.

Usually the reason one or more pots in the same tray need more water is because your surface isn’t level and the water will pool at one end of the tray. Be watchful for this condition and prop up one end of the tray if needed to ensure that every pot is getting enough moisture.

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As the seedlings grow, the more water they will need. When they are tiny, you may only have to check them every few days, especially if you are using a humidity dome. The more leaves the plants have, the more often you will have to check them. Depending on conditions, you may have to check on larger plants more than once a day.

Hardening Off Seedlings for the Garden

One of the most important things you can do is to harden off all your delicate seedlings. If you aren’t careful, you can almost watch them wilt and die before your eyes.

The hardening off process slowly acclimates your plants to the outdoor environment. Think of it as getting your plants used to the sun and wind.

You can help your plants getting used to air movement almost from the very start. Use a small fan to gently blow air across the trays where the seedlings are growing. The movement this causes helps develop stronger stalks and reduces the chance of breakage due to weak stems.

Small fan with clip
A fan such as this 6 inch fan with a clip for attaching to your shelves works very well for helping grow stronger seedlings before they meet the harsh, cruel world outside. (Click the photo for more info.)

If you don’t have access to a fan or have nowhere to attach it where it will do any good, consider brushing the seedlings once or twice a day. A gentle back and forth stroke across the top of the plants will simulate using a fan and give you similar results. There really is no way to duplicate wind conditions, and you’ll still want to protect your seedlings from strong winds no matter what you do, but a fan or brushing will help develop stronger stems. And anything you can do to reduce problems with your seedlings as you introduce them to the cold, cruel world, is better than nothing.

Tomato seedlings starting to acclimate to the outdoors. Note the filtered sunlight instead of bright, full sun to start the hardening off process.

Because the sun is so much more intense than any grow light we can buy, you’ll need to be extra careful with how long each plants are exposed to unfiltered sun. Young seedlings that have not seen the sun will experience leaves that burn in sun. Always start them out in filtered shade and then move them to more full sun little by little over 1-2 weeks.

This is when a cold frame or greenhouse can come in really handy. Typically, the enclosure will provide a better environment that fosters the hardening off process. For example, my cold frame is made of double-wall polycarbonate panels and I place my seedlings in the cold frame as soon as the thermometer inside the cold frame shows temperatures over eighty degrees Fahrenheit during the day.

Cold frame in the snow
My cold frame in the winter. It is amazing how it protects young plants.

Because it is a protected environment and also helps prevent the plants from drying out too quickly, I don’t worry that the cold frame is in full sun all day. I do worry about venting when the internal temperature of the cold frame gets above ninety degrees, but an automatic vent will help maintain the proper temperature. So my hardening off process is nearly complete only by using the cold frame.

Personal Rise Garden
Want to grow everything inside from beginning to end? This personal garden from Rise Gardens is an excellent option.

Once the days are warm enough, I’ll leave the top of the cold frame open all day. Then I’ll move the plants to the garden to get ready for planting. So in the end, my plants will have been outdoors, inside or outside the cold frame, for at least a month before planting time.

Transplanting Seedlings

The time has finally arrived to transplant your beloved seedlings. The danger of frost is gone. The days are warm and the nights are generally above fifty degrees Fahrenheit. For me in Zone 4, I’m lucky if the nights are above forty degrees, so all growing conditions are a bit different.

It will be better to delay planting directly in the garden if you have a heavy rain or frost in the forecast. Muddy soil will drown the roots and kill your plants within a few days. Frost will kill them overnight. It is better to wait a week than to try and hurry things along. I’ve spoken to many a gardener who told me that the plants they planted late, outperformed the plants that had to struggle through environmental conditions that were not optimal.

Digging with Hori Hori garden knife
Transplanting in the garden is when the Hori Hori knife comes in so handy. Learn more about the Hori Hori here, or you can purchase it directly from The Negligent Gardener here.

Before transplanting, be sure you have determined where in your garden each seedling is going to go. How are you going to space your plants? Will you use an intensive method such as Square Foot Gardening? Or do you have room to plant them further away from each other in rows?

I usually use a combination of both of these methods and it is perfectly fine to experiment with your own spacing as you go along. Search online for spacing charts or you can use one of my guides to get started.

Minimizing Transplant Shock

The scourge of transplanting is the shock it puts on your seedlings. Transplant shock will wilt the leaves temporarily and you think they will never recover. Every now and then, seedlings don’t recover, but don’t get discouraged.

The most important thing to do during transplanting is to provide enough water. Click here to see a watering can with a gentle spray. I have one of these and they put out a lot of water but don’t damage young plants.

First, dig a hole slightly larger than the pot that the seedling is currently growing. You can add fertilizer to the hole if you prefer but be careful about which fertilizer you use. At this point, I would recommend only organic fertilizers because they are least likely to burn the roots. Even when using organic fertilizers, place the recommended amount in the planting hole as described on the box or bag of fertilizer. Then mix it with a shovel full of soil in order for less fertilizer coming into direct contact with the roots of the seedlings.

Because roots will want to grow out to the sides more than growing down into the soil, it is also good practice to place some fertilizer around the edges of the planting hole. If your hole is slightly larger than the pot, you will be filling in soil between the roots and the fertilizer and won’t burn the roots.

One of the best things you can do is to add straight well-rotted compost to the planting hole. This won’t burn the roots and will reduce your worry at the same time. I have been adding a good heaping of my worm compost to the planting hole for many years. (Learn more about composting with worms here.) Compost will also help retain moisture and thus reduce transplant shock.

Now it’s time to fill the hole with water. Depending on how quickly your soil drains, you may even want to fill it more than once. This will ensure that the soil is well moistened, giving those roots a good start in the garden.

Remove the plant from the pot and you will likely note that a lot of roots are present around the outside. This is not unusual for seedlings that have been growing in small pots for so long.

Asparagus roots
Gently straighten out the roots with your fingers to make it easier for the roots to grow into the soil.

Disturb these roots as little as possible. This means that the roots should be exposed to the air for only about ten seconds. If you have your hole prepared, have added fertilizer, and filled it with water, this is easy to do.

One thing that may be needed is to gently tease the roots so that they aren’t winding around the root ball. All this takes is straightening out the very bottom roots so the root ball isn’t the same shape as the pot. It doesn’t take much and will help the roots stray out in the right direction where they can reach nutrients more readily.

Some gardeners will use a trowel or similar small hand tool to disturb the roots along the outside of the entire root ball. I don’t think this is entirely necessary. I use my fingers to just straighten the roots on the bottom and sometimes on the sides of the root ball. You don’t have to be drastic at all and remember to then get the plant in the prepared hole as quickly as possible.

Once you have your seedlings planted, give them another good watering from the top. This next day or two will be the most important time to pay attention.

Check on the seedlings two or three times a day to check for any wilting and get them more water if they are showing signs of stress. It won’t take long for the roots to grow and get established, but you have to intervene as soon as possible or the seedlings may not be able to recover and will die.

Growing from Seed

Growing from seed is a process that you develop over time. You should not be intimidated to give it a try. If it’s your first attempt, start small with only a few seeds or you may be overwhelmed. Reap the rewards of enjoying the changes in your seedlings every day. Watching a tiny tomato seed grow into a huge vine is just one more way to enjoy the wonders of nature.


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