Are you trying to grow different vegetables, herbs, and flowers from seed, only to have them not germinate, look weak, or downright unhealthy?

Or worse, are your seedlings just randomly dying with no warning?

Take comfort in knowing that seed starting is a common challenge among new gardeners.

I had this happen to me when I first started growing my own plants from seed. I started four trays of different vegetables and herbs, with visions of a lush green garden and tasty harvests.

Of that first batch, the only plants that germinated was one borage plant and one basil plant.

Needless to say, I was crushed.

I made a few adjustments, and tried again with better germination but extremely leggy seedlings that weren’t healthy at all.

Fast forward to today, and I’m the proud caretaker of a thriving one-acre garden, where the vast majority if plants I start from seed each year. This transformation didn’t come overnight - but through research, testing, and adjusting, I refined my seed starting techniques.

Here’s what I did the next year (and every year since) to be certain my seedlings get the best start they can for ultimate health and resilience.

You’ll learn how to:

• identify and prevent damping off (when seedlings randomly keel over and die)
• Understand legginess in seedlings and how to grow strong, sturdy plants instead
• Select the best seed starting equipment to set your seeds up for success from the very start
• Implement best practices in sowing vegetables, herbs, and flowers from seed indoors

With these tips, you’ll give your seedlings the best possible start, and be on your way to a garden that’s not only alive - but thriving.

→ Here’s what you must do to be successful with starting seeds indoors:

1.Sanitize your seed starting equipment: If it’s your second year with your equipment, clean everything with soapy water. This helps prevent diseases like damping off.
2. Bottom watering trays: Use trays designed for bottom watering to encourage strong plant growth and discourage overwatering.
3. Grow Lights: Be sure your LED lights are close enough to your plants so they don’t have to stretch. This prevents legginess in seedlings.
4. Mimic the Wind: Run a fan on your seedlings a couple times a day for strong stems and better air circulation.
5. Thin your Seedlings: Thin seeds so there is only one plant growing in each seed cell.
6. Potting and Transplanting: Know when to pot up your seedlings or transplant them outdoors.

The Basics of Seed Starting

Select High-Quality Seeds:

Quality is key when you select your seeds. Reputable seed companies conduct rigorous germination tests to ensure their seeds meet high standards. New gardeners particularly benefit from these quality seeds, though small-scale vendors can offer unique varieties.

→ Check out my list of the best seed shops. These sellers focus on organic practices and offer robust seeds. I’ve sorted them by region so you know your seeds are adapted to your climate.

Start with fresh seeds:

For beginners, fresh seeds—typically less than a year old—greatly improve germination chances. Seasoned gardeners might experiment with older seeds, but newcomers should seek out the freshest options.

Seasonal Timing:

Follow seed packet instructions for the best seed planting time. Too early, and seedlings may become overgrown in their pots; too late, and they might not mature before the cold weather arrives.

Double Sowing:

If you’re just starting out or have had struggles in the past, it can be helpful to sow two seeds to increase your chances of germination and healthy plants. As you gain experience, you will learn which seeds you only need to single sow.

Label it!

Whether you write the info down on popsicle sticks, a spreadsheet, or masking tape stuck to the side of your seed starting trays, it is essential to label your seed trays.

Here’s what you should put on your labels:

• plant + variety name
• date sown
• days to germination
• days to maturity

Here’s an example for a label for Thai Basil:

T. Ba 4/21 7 60

That’s my code for “Thai Basil, sown April 21st. This should germinate in 7 days. I’ll get my first harvest in 60 days.”

These details help me to quickly assess a plant’s progress and troubleshoot if needed.

Equipment and Setup for Seed Starting

Containers and Trays for Healthy Growth:

I’m obsessed with the seed trays from Epic Gardening. After seeing how much waste I was creating with flimsy and poorly made seedling trays that would just crack and break after one season, I’m pretty impressed with how the seed cells and trays from Epic are holding up.

I bought a 120 pack of the 6-cells the same week they were launched three years ago, and they are still going strong.

Not only are they well-made, but they allow for optimal seed starting success.

• Set up for bottom watering: Add the water to your seed starting tray instead of overhead watering. This prevents damp leaves, which would otherwise lead to diseased plants. It also prevents overwatering - the soil will wick up the amount of water it needs.
• Slots for air-pruning: There are holes and slats on the 6-cells so that the roots of the seedlings “air prune.” Instead of continuously growing in an unhealthy way, the roots cut themselves off when they reach the air. Seedlings will be healthier this way.
• Easy seedling removal for transplanting: You can easily push the seedling out from the bottom of the six cell, because the hole at the bottom of the tray is not pencil-sized. This means you can transplant your seedling into the ground without disturbing it too much.

For most plants, the 6-cells are a great size.

Sanitize Your Seed Starting Equipment:

You can skip this if you are starting with brand new seed trays. Otherwise, I highly recommend thoroughly cleaning all of your equipment.

This step isn’t just to remove last year’s dirt and grime - it’s mainly to remove any bacteria remaining from last year that could transfer over to your seedlings this year.

For example, damping off - when your seedlings just snap at the bottom and fall over dead - can be transmitted to your seedlings in this way.

While I admit that it’s tedious to wash each cell of dozens of seed starting trays, it’s a crucial step for success.

I first soak my equipment in hot soapy water. Then I rinse them off well.

Next, I clean the trays with vinegar. I use a rag for this, and I switch out the rag every few trays or so.

I’ve found that using paper towel for this will lead to a lot of waste, and a facecloth is too thick to really get into the nooks and crannies of the seed starting trays.

Lighting Essentials: Positioning LED lights for sturdy growth

There are tons of grow light options out there. I keep things simple and affordable with LED shop lights. They are also very efficient to run.

One way to avoid legginess in your seedlings is to place the seed trays close to your supplementary lights.

If you’re growing seeds in a windowsill, the addition of an LED grow light will skyrocket your results in most cases.

If your lights are more than a few inches above your seedlings, raise the seed tray up until the seedlings get taller.

I have my LED lights on strings, inspired by this set up here. I can lower and lift them with ease, depending on the growth of my plants.

The Right Seed Starting Mix:

Seed starting mix should be fine and soft. If your seedling mix has many pieces of organic matter bigger than a couple centimeters, it’s best to sift it out for best results.

→ For sustainability’s sake, try to find a seed starting mix that does not contain peat. Read more on the environmental benefits of peat bogs and why we need to conserve them here.

Create the Ideal Environment

Temperature and Humidity:

Temperature is an important factor in seed germination. For most seeds, a temperature of 60 degrees F is ideal. Some seeds, like pepper seeds, are notorious for being slow to germinate because they like temperatures even warmer.

Some folks will buy heating mats for their seedlings, which are placed under seed trays and generate a small amount of heat. This can be helpful if you’re starting seeds in a room that does not receive supplementary heat in the winter.

I have success with placing pepper and eggplant seeds near my wood stove, which we usually only use at night. Immediately when seeds germinate, I move them into the seed starting room so they have access to the grow lights.

Keep a humidity dome on seeds until germination. Then, keep the humidity dome off to ensure proper air circulation and reduce disease from too much moisture on leaves.

Air Circulation:

A fan is an essential component of your indoor seed starting setup. This is for two reasons.

First, the breeze from a fan simulates the wind that a seedling would encounter in nature. The wind causes the plant to move a little from side to side, and this strengthens the seedling’s stem.

If you don’t have a fan running, your seedlings can appear leggy even though they have enough light.

Second, air circulation helps to prevent diseases like damping off.

Set up a fan on its lowest setting so that all of your plants move slightly. I run my fan twice a day for 15 minute intervals.

If you’re savvy, you can even set up an automatic timer to ensure that the fan runs daily.

Step by Step Guide to Starting Seeds Indoors

Phase 1: Sowing

1. Set up your soil: You want your soil to be damp - not sopping wet, but also without any dry spots. I put my soil into a large bowl or bin to mix water in.
2. Add soil to your seed trays: Fill your trays to the top. Lightly press the soil in to be sure that each cell is totally full.
3. Sow your seeds: A general rule of green thumbs for vegetable seeds is to plant the seeds twice as deep as they are tall. So a squash seed needs to be buried deeper than a beet seed, for example. Double check seed packets for herbs and flowers - some need to be surface sown.
4. Label your seeds: Don’t skip this step!
5. Place a humidity dome over your seed cells: I consider this step optional.
6. Monitor water levels: Check in with your seed trays daily. Avoid overwatering and avoid overhead watering, especially after germination.
7. Watch and wait: When you see those first sprouts, it’s time to move into phase 2.

Phase 2: Post-germination

1. Remove humidity dome
2. Be sure grow lights are close enough to seeds
3. Thin seedlings so that the strongest one remains in each seed cell
4. Run a fan twice a day for 15 minutes
5. Monitor water levels and always bottom water. Don’t over water your plants.

Phase 3: Maintenance + Transition

1. If your plants are growing too big for your seed trays, it’s either time to transition them outside or pot them up.
2. If your area still has a chance of frost, pot up your plant into a bigger pot. Usually a 5-6 inch pot is sufficient. Bury the seedling up to an inch below its lowest leaves.
3. If you are clear from future frosts, start to transition your seedling to the outdoor world. This is called “hardening off.”

To do this, let them hang outside in a partly sunny spot for a couple of hours each day, gradually increasing over the course of a week. Still in their seedling trays, let them then spend a night outside before transplanting them into their new home. Water the transplant in well.

You did it!

Common Seedling Problems and Solutions:

Problem: My seedlings looked fine, but then they just dropped dead. It looks like someone snapped them at the base of their stem.

This is called damping off. Here’s what to do to fix it:

• Toss your dead seedlings and soil. I know. It hurts. But it will prevent future issues.
• Sanitize any trays that came into contact with your diseased plants.
• Start over again, and be sure to bottom water your seed trays and run a fan twice a day for 15 minutes each.

Problem: My seedlings are leggy, spindly, and weak. Can I save them?

You might be able to! However, if it’s early enough in the growing season, I’d recommend starting over. You could also start off by sowing some backups incase your fix doesn’t work out. If your plants end up okay, then you’ll have extras to share.

As soon as you notice spindly seedlings, gently repot them and bury the stem so that 2/3 of it is under the soil level.

Lower your grow lights so they are 2-4 inches above your seedlings, and run a fan twice a day for 15 minutes each.

If you sowed more than one seed per cell and they all haven’t germinated yet, you can also pull out the leggy seedlings and wait for the other seeds to germinate. The same applies if you haven’t thinned your seedlings yet. Thin out the leggiest one and keep the shorter one.

Also note that not thinning your seedlings soon enough can cause them to get leggy, because they’ll compete for sunlight.

Problem: There’s green fuzz growing on my soil, what is that and is it bad?

It not necessarily bad, but it does point to an issue of over-watering and poor air circulation.

This green stuff is fungus, which can be a great place for fungus gnats to live. While the fungus and fungus gnats won’t cause much trouble if you catch things early, they can quickly become an issue.

It’s still a good idea to water a bit less, be sure you’re bottom watering, and that you have your fan running at regular intervals daily.

I’ve had luck with letting the soil dry out (not enough to harm the plants), and then pouring a strong infusion of chamomile tea on the green spots. This is the only time to be watering overhead. Avoid getting the leaves of your plants wet. Chamomile tea is anti-fungal and can help resolve this issue. Continue treatment until it resolves, let the soil dry out between treatments each time.

Problem: My seeds aren’t germinating at all! What’s going on?

Oh, I’ve been there. For me, I was way over-watering my soil. Like, way way too much water. So be sure you’re not over watering your seeds.

Another issue I’ve had is not knowing that some plants, especially perennial plants, need to go through a process of cold stratification before they will germinate.

I have a full guide about cold stratification here, where I list out which plants need to go through a cold treatment and for how long before you sow them.

The basics of it, though, is that if perennial herbs (like nettles and lavender) or perennial flowers (like lunaria or milkweed) won’t germinate, it’s likely that your seeds need to experience a winter before they’re triggered to sprout.

Problem: Well all my seeds germinated. How do I choose which seeds to thin? Do I really need to thin them?

It’s hard to see your hard work pay off only to go through and determine the fate of your well-cared for seedlings one by one.

I still find it challenging, but I remind myself that the seed that remains will grow better and stronger for it.

I like to pick plants that meet most of these qualifications as keepers:

• They are in the center of the plant cell instead of on the edge
• They are a deep green color
• They aren’t too leggy from lack of light or competing with other plants
• They are on track development-wise

If you have two plants in a seed cell that look fantastic, you’ll likely just need to pick at random.

If your thinned seedlings look really good, and you are able to extract them carefully from the soil, you can replant them into their own seed cells. I’ve done things with a variety of plants before with a pretty high success rate.

Conclusion: Harvesting the Rewards

• The joy of watching your seedlings grow into thriving plants
• Encouragement for continuous learning and improvement

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