Starting Seeds Indoors: A Step-by-Step Guide

Starting seeds indoors under lights can seem intimidating. However, this step-by-step guide demystifies the seed starting process and helps you get started with confidence.

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Who Should Start Seeds Indoors?

Starting seeds indoors under lights is quite the process, but don’t worry. It’s simple when you follow these instructions, and it gets easier with practice!

However, there is an initial investment to acquire the equipment and materials, so if you’re new to gardening or are super-busy, then it might be better, initially, to skip this step.

Instead, you can start seeds out in the garden when the weather warms up (for some crops) and buy seedlings from a local farmers’ market or nursery for those crops that need more time to develop.

Some gardeners start seeds in south-facing, sunny windows rather than under lights, but success with this method can be inconsistent for a variety of reasons such as lack of daylight hours, extreme temperature fluctuations, and a reduction in UV light by the windows themselves. Modern windows may only transmit 25% of ultraviolet light, while older, plain-glass windows may only transmit 80% of light.

Check out this comparison of seedlings grown on a windowsill vs. under lights.

If your budget doesn’t allow for starting seeds under lights just yet and you intend to use a windowsill, heat mats can be extremely helpful.

Ultimately, you won’t find two gardeners who start seeds indoors exactly the same way, but the following is the system that has worked for me for many years.

When to Start Seeds Indoors

For most people, your frost dates determine when to start seeds.

Once you know your frost dates, you can set a schedule for starting seeds indoors using my article When to Start Seeds: Your Guide to Spring Planting. If you’re starting seeds for fall, check out When to Start Seeds: Your Guide to Fall Planting.

You may also want to check my Year-Round Gardening Guide which details to-do lists for each month.

Grow a garden that’s both productive and manageable with my Complete Garden Planning System, which includes practical tools for planning your season from seed to harvest.

Get Started #1: Set up Shelves

The shelving unit you choose determines a lot of things, such as the size of your lights as well as how much of the other equipment listed below you will need.

I use wall-mounted wire shelves in my mudroom. Throughout much of the year, these shelves act as a root cellar where I store harvested vegetables such as garlic, onions, potatoes, sweet potatoes, and winter squash. After the new year, I condense my storage vegetables and make room for starting seeds on these shelves.

If wall-mounted shelves don’t work for you, try building your own wooden shelves or purchase a free-standing, 6-tier wire shelving unit.

The reason I like this particular wire shelving model is because each shelf can hold two standard nursery trays (22″), which is uncommon for this style of shelving. In total, this unit can hold 10 nursery trays, double what other 6-tier shelving units can hold. (The top shelf is for storage.)

Why buy two shelving units when you can do it all with one? Just be sure to compare the height of your ceiling to the dimensions of the shelving unit before purchasing.

I think it’s easiest if you can access both sides of the shelves, which is why I recommend the free standing units. However, I’ve managed fine with single-side access to my wall-mounted shelves.

Get Started #2: Select Lights

The type of lights to use for indoor seed starting is a topic of great debate. Many experienced growers swear by inexpensive shop lights, while others insist that the best quality comes from specialized grow lights.

In reality, there are three reasons why this debate continues.

Firstly, there’s a difference between the needs of commercial growers growing exclusively under lights and home gardeners who grow seedlings to a certain size before transplanting them outside.

Secondly, lighting technology is always changing, so a model that may have been expensive and inconsistent a few years ago may now be leading the pack in affordability and/or reliability.

Thirdly, the science with regard to lighting is extremely technical and often misunderstood. As an example, check out these myths about LED grow lights.

If you already have fluorescent shop light ballasts, then full-spectrum fluorescent tube lights should be sufficient. Be sure the ballasts fit the width of your shelving unit. Typically you will need two ballasts, side by side for each shelf, as pictured below. 32 watt, T8 bulbs have worked pretty well for me.

Go ahead and keep using those old shop lights if that’s what you have. However, replace the bulbs at least every other year (even if they haven’t burned out) in order to keep sufficient brightness for growing.

You’ll also need screw hooks for wooden shelves OR s-hooks for wire shelves (2 per fluorescent light fixture) to hang the lights from the shelving unit.

Here are some more tips for growing with fluorescent lights.

Are LED Grow Lights Better?

LED grow lights are still more expensive than the old fluorescent shop lights, but they’ve come a long way. To date, they generally provide a superior seed starting experience and are a better investment if you’re buying all new equipment.

LED grow lights now mimic sunlight more closely, with smaller and lighter units that are extremely energy efficient and long-lasting. They even have white-yellow lights now, which are more pleasing than the “blurple” lights of older LED technology.

Here is the LED grow light that I recommend because it’s the least expensive model I’ve seen with the most coverage. The dimensions of this light fixture are only 11.8″D x 11″W, but the light coverage spans 2.5′ x 2.5′.

You would need two of these lights for each shelf of the 6-tier unit I recommend above, which equals 10 lights in total. This is obviously a significant expense, so start with the equipment you have and add/improve over time.

Get Started #3: Select Seed Starting Mix

There are two big issues to think about when selecting a seed starting mix: sustainability and herbicide contamination.

Let’s take a brief look at each.

With regard to sustainability, there are two materials widely used as the main ingredients in bagged soils and soilless mixes: peat moss and coconut coir.

As we’ve learned about peat bogs being destroyed in Canada to cultivate peat moss for gardening products, coconut coir has emerged as a “sustainable” alternative.

Although it isn’t a 1:1 replacement (peat is superior in performance), coir works pretty well.

Unfortunately, the coir industry is not so environmentally friendly and is polluting and depleting the environment where it’s made.

In addition to the peat vs. coir debate, many bagged soils and potting mixes contain compost as a main ingredient, which is quite often laced with persistent herbicides.

These poisons can damage your seedlings and garden for years.

If peat moss, coconut coir, and compost are all “bad”, what can you do?

First, remember that you have the most control over what you do on your own site.

Learn about how herbicides can contaminate your garden and compost (even if you don’t use herbicides yourself), and seek to keep them out. Then use your own compost in your gardening activities, including as a seed starting medium.

In addition, rather than throwing old potting soil in the compost or trash, consider reusing it as a sterilized seed starting mix. Here are some tips for sterilizing potting soil and compost for seed starting.

Second, buy a seed starting medium that you feel is the best choice for you, using (and reusing) it wisely.

Don’t be fooled by bagged soils that have “Organic” on their label without indicating that they’ve been verified and approved for organic agriculture by a third party.

If a seed starting mix contains compost, rigorously interview the company about their practices to avoid herbicides. That’s how I found Tilth Soil’s “Sprout” seed starting mix, which is approved for organic agriculture and can be used for both seed starting as well as potting soil for transplants.

Currently, coconut coir seems to be the most widely available main ingredient for a seed starting mix that is approved for organic agriculture. If you can’t get the “Sprout” mentioned above, try this runner-up seed starting mix. It’s compressed, so lightweight (easier to ship/fewer emissions) and requires less packaging.

Supply List for Starting Seeds Indoors

In addition to shelving, lights, and seed starting mix, the following supplies make the whole process run smoothly. You won’t have to buy most of these items ever again! Check out my one-stop Amazon shop to see all of this equipment in one place.

• Aluminum foil, Mylar reflective film, or mirror for low light areas
• Clip fans (one for each shelf)
• Seedling heat mat with thermostat (1-2 per shelf)
• Thermometer/humidity monitor
• Programmable power strip
• Waterproof table OR shop-style work bench
• Standard nursery growing trays (no holes – 22”x11”)
• Plastic seed starter cell packs OR reduce plastic with a soil blocker + nursery trays (with holes)
• Seeds (I check Botanical Interests first.)
• Large galvanized steel tub
• Plant markers
• Permanent marker
• Small watering can
• Garden gloves (optional)
• Pencil (sharpened)
• Plastic wrap (Saran-style) OR plastic germination domes to fit nursery trays
• Potting soil: Tilth Soil’s “Sprout” (all-in-one seed starting and potting soil mix) or Nature’s Care potting soil
• Plastic pots
• Cinnamon spice shaker (optional)
• Fish & Seaweed Fertilizer
• Garden Scissors

Your Step-by-Step Guide for Starting Seeds Indoors

Step 1: Assemble the shelves.

Assemble the shelving unit and set it in a level spot, in a room with as much ambient light as possible. My seed starting room is in the basement with no ambient light, so I cover the walls with aluminum foil (shiny side out) to reflect the light. Mylar reflective film is less flimsy, while a large mirror can work, too.

Step 2: Hang the lights.

Hang the lights using screw hooks or s-hooks, and mount a clip fan at the end of each shelf.

Step 3: Manage the temperature and humidity.

Set out the heat mats as well as the thermometer on or near the shelving unit.

The ideal soil temperature for starting seeds indoors is 68-86° F, which is usually attainable with ambient heat in the house and the supplemental heat mat. The accompanying thermostat can ensure you keep your seedlings within a healthy temperature range for germination.

Because my seed starting operation is in a small, enclosed room, I use an extra thermometer and humidity reader to ensure good conditions. A small space heater warms the air in the enclosed space.

As for humidity, seedlings prefer 50% to 70% humidity. Cool indoor air is usually dry, so keep a spray bottle of water in the room and mist the air several times per day (not the seedlings).

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Step 4: Manage the power source.

Mount the power strip and organize the cords with twist ties so they’re out of the way for regular seedling maintenance, and away from possible water spillage.

Plug the light fixtures into the timed outlets and the fans and heat mats into the always-on outlets. No need to turn anything on yet, though.

Step 5: Ready to start seeds? Assemble the materials.

Collect your trays, cell packs, seeds, seed starting mix, steel tub, plant markers, permanent marker, watering can (filled), garden gloves and pencil near your work table.

Note about reducing waste:

Don’t be afraid to use materials that you already have around the house. For example, I usually end up rooting through my kitchen and using things like metal roasting pans as drainage trays.

Plastic food-safe containers that you normally recycle are just fine to use as either drainage trays or seed starter pots depending on their size. Also check out this easy way to make upcycled seed starter pots. 

Step 6: Prepare the planting medium.

Fill the tub with seed starting mix and add water, one gallon at a time, mixing just until the soil medium clumps together. It should feel like a wrung-out sponge: If water can be squeezed from it then it’s too wet. To remedy, add more soil.

Excess planting medium can be saved. When you’re finished starting seeds, let the medium dry out before storing it.

Step 7: Prepare the cell packs.

Fill each cell of a cell pack to the top loosely with the seed starting medium. Pack it in firmly, so that now each cell is only one-third to 2/3 full.

Then fill each cell again loosely to the top. This time, press lightly rather than packing down firmly.

Step 8: Choose a seed packet to begin starting seeds indoors.

Select a seed packet to work with and consult your garden plans to figure out how many seeds to start. Always start a few extra just in case.

Step 9: Plant the seeds.

Plant seeds twice as deep as their size, at least two per cell in opposite corners. Use the pencil to push the seeds in, then lightly press the soil on top so that the seeds are covered.

Press tiny seeds into the top, such as lettuce seeds, rather than covering them.

Step 10: Label the cell packs.

Label each cell pack with a plant marker.

Step 11: Fill the drainage tray with cell packs.

Place the cell packs in a drainage tray (the nursery tray without holes).

Step 12: Water the seeds in.

When the drainage tray is full of cell packs, water each cell very lightly from the top to ensure the seeds have made contact with the soil.

Step 13: Cover the trays for germination.

Cover the tray with plastic wrap or a clear germination dome and set on a heat mat. This keeps seeds warm and moist to increase germination rates.

Step 14: Start the rest of your seeds.

Continue the process until all seeds have been started and all trays have been covered and set on a heat mat.

Step 15: Turn on the heat mats.

Make sure all heat mats are on. Lights and fans are OFF until the seeds have germinated.

Step 16: Check daily for germination.

Each day check for germination, briefly lifting the plastic wrap or dome to allow some condensation to escape. Once seeds have sprouted, immediately remove the plastic covering.

Would you like to grow more food with less effort? Check out my mini guide, The Permaculture Inspired Vegetable Garden.

Step 17: Set the lights on a timer.

Once the seeds have germinated and the covers have been removed, turn the lights ON and the fans on low.

Turn OFF the heat mats, unless the temperature in the room regularly dips below 68 degrees F.

If you’re short on heat mats, prioritize their use for the following heat-loving crops: eggplants, peppers, okra, watermelon, and tomatoes, which prefer temperatures to be closer to 80 degrees F.

Set timers for the lights on the power strip:

If your seed starting room has ambient light from nearby windows, allow your plants to follow the natural cycle of daylight hours. To do this, program your lights to turn on at sunrise and off at sunset on the longest day of the year in your region (June 21st in the northern hemisphere).

For example, in my region I would turn the lights on at 6am and off at 9pm, for a total of 15 hours of light. This keeps my plants on a natural cycle, and I like to believe it eases their acclimation to the outdoors.

Note: If you’re starting seeds indoors in a windowless room with little-to-no ambient light, OR if you’re using fluorescent shop lights, I suggest keeping the lights on 24 hours a day. In this case, the timer isn’t necessary.

Step 18: Position the lights.

Using the adjustable chains on the light fixtures, position the lights 10 inches above the seedlings. Adjust the lights regularly as the seedlings grow.

Step 19: Water regularly.

Once your seeds have germinated and are under the lights and fan, check frequently for dry soil. Let the soil mix dry completely before adding water to reduce the chance of “damping off”, a problematic fungal disease in seedlings with too much moisture.

To water, remove one cell pack from a drainage tray and fill the tray halfway with water using the watering can. Replace the cell pack.

Set a timer for 10 minutes, then check all the cells for moisture. When the cells are all sufficiently moist, carefully dump out the excess water from the drainage pan.

Watering from below instead of above reduces the incidence of damping off. If you have an outbreak, immediately remove the affected plants and put them in the garbage.

Sprinkle cinnamon on the soil of the remaining healthy seedlings to minimize the spreading of the damping off fungus. Cinnamon is a natural anti-fungal that won’t damage healthy seedlings.

Step 20: Thin crowded seedlings.

The seedlings must be thinned once they’ve produced their second set of leaves (their first set of true leaves). If there’s more than one seedling in a cell, remove all but the strongest 1-2 most vigorous seedlings.

Use garden scissors to cut off the weaker and more slow-growing seedlings at the soil level. DON’T PULL THEM OUT, as doing so may disturb the remaining young seedlings.

Step 21: Fertilize young seedlings.

The first set of leaves of a seedling acquires nutrients from the seed itself, requiring no fertilization on your part. However, as the seedling grows, it develops its first set of “true” leaves. These true leaves are a sign that the seedling has used up its stores of nutrients in the seed and requires outside fertilization.

Since most seedstarting mixes are free of nutrients, you’ll need to fertilize. To water the seedlings with fertilizer, add one tablespoon of fish fertilizer per one gallon of water and mix well, following the directions on the label. Use as part of the regular watering schedule.

Step 22: Re-pot growing seedlings.

If seedlings outgrow their cell pack before it’s time to plant them outside, then you’ll need to transplant them into a bigger pot.

For seedlings that have more than two sets of true leaves, check your planting schedule. How long until you plant them outside? If you have more than one week until transplant time, re-pot them using potting soil (not the seed starting mix).

Keep in mind that bigger pots take up more space and might not all fit under the lights. Try to keep them in rotation between the lights and nearby sunny windowsills.

Step 23: ‘Harden off’ the seedlings before planting.

For seeds started indoors, there is a key step in transitioning them to the outside world. One week before transplanting them outside, they must go through the ‘hardening off’ process to gradually be acclimated to sunlight, temperature fluctuations, and other conditions that can be shocking.

Protect them from hard rain, heavy wind, or extreme temperatures during the process. Water frequently, as needed, but do not fertilize. Partial sun is better than direct, full sun. Daytime temperatures should be in the 60°s F or warmer.

If extreme temperatures or heavy rain is in the forecast, delay the hardening off process.

• Day 1: Place the seedlings in a shady spot outside. Don’t forget to bring them inside at night!
• Days 2-4: Place them in a sunny spot for 2-3 hours, adding two additional hours daily. Return to the shade for the rest of the day, and bring them in at night.
• Day 5: Increase to 9 hours of sunlight. Can remain outside at night if temperatures are in the 60°s F.
• Day 6: Increase to all day in the sun and overnight outside.
• Day 7: Plant in the garden if no extreme weather is on the horizon. If it is, wait it out.

Step 24: Transplant seedlings into the garden.

Prepare the area that you intend to plant in by loosening the soil and amending it with homemade compost, worm castings, or other soil amendments.

Turn the pot upside down and firmly tap the pot against the palm of your hand. Push the seedling out of the container from the bottom. Never pull on the stem of the seedling to remove it. Transplant it into the garden.

Water the plant deeply, using a diluted fish fertilizer, and check on the newly planted seedlings regularly.

Step 25: Protect the seedlings from cold.

If temperatures take a sudden dive, be prepared to cover newly planted seedlings with row cover, buckets, plastic sheets, a cold frame, or anything else you can find. A wire A-frame with a plastic sheet thrown over it works well.

FAQ: Oops, I’ve missed the seed starting date. What can I do?

If you’ve missed seed starting for a particular crop, have no fear. There is often a window of at least four weeks (and often more) to start seeds. Consult my article When to Start Seeds: Your Guide to Spring Planting for details. Beyond that, check local nurseries for seedlings.

And that sums up starting seeds indoors. Will this guide help you give it a try?

READ NEXT:

• 9 Organic Soil Amendments for Growing Vegetables
• What to Plant Now: February Garden Guide
• Year-Round Gardening

>>> Get my free 19-page Guide to Organic Soil Amendments for more ideas: