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Seed Starting
Published August 31, 2022 by Danielle Boss

The Best Seed Starting Trays to Start Seeds Indoors

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seed starting
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seed starting trays

A Quick Overview of Seed Starting

Starting seeds for your garden is one of the most exciting things you can do. To see something so small grow into a beautiful and productive part of your garden is magical. But for a lot of new gardeners, it can seem overwhelming to start. How exactly do you do it? How do you know what materials to use? How do you know when your seedlings are ready to be planted outside?

Well, Gardenary is here with plenty of answers and information all about starting seeds! Check out these articles:

In this post, we're going to take a deeper dive into the different seed starting setups, in particular the trays and kits. There are so many options to pick from, so let’s take a look at what all you can use!

seed starting supplies

What Should Your Seed Starting Setup Look Like?

When starting seeds indoors, just remember that you are trying to mimic the outdoors as much as possible. You'll want the temperature to be warm and the area to have perhaps a little humidity, if possible. There also needs to be some air flow and light. While some people choose to use natural light, your seedlings are going to grow weak and leggy unless they're in a greenhouse with full overhead sunlight. Being placed on a windowsill is often not enough. Your best bet is to grab a grow light to use in whatever location your seeds will grow.

I have been starting seeds indoors for years now, so I will show you an example of how I started versus how I'm doing it now: In the beginning, I used styrofoam cups placed on a baking tray, with a clip-on grow light, in my office. Super simple and cheap, but effective! I didn’t need to start a ton of seeds because my growing space was little, so this worked well enough.

As my garden expanded, I invested in more materials in order to start more and more seeds. Now I have an extra bedroom closet I use, with a shelving unit, attached grow lights, and seed trays. This setup was more labor intensive and expensive to get going, but I can start a lot more seeds this way, and by now, I know the investment is worth it.

seed starting how it started vs how it's going

What Materials Can You Use to Start Seeds?

While my personal preference is a seed starting tray, there are other things you can use to get going. Let's look at some of the advantages and disadvantages of different materials.

Seed Starting with Household Items

Many gardeners trying to reuse what is already in their home will start seeds in eggshells, egg cartons, rolled-up newspaper pots, yogurt cups, toilet paper rolls, and more.


A lot of these materials are biodegradable, so the whole pot can be planted directly into the soil. That is definitely a benefit, as is the ability to repurpose something that would otherwise be tossed in the trash.


I have tried a few of these items and either found them to be too small or had them decay and break down before I could plant my seedlings outdoors.

Seed Starting with Peat Pots or Coco Coir Discs

These are pre-made pots, trays, and discs (also called pellets) sold widely online and in stores.


They're biodegradable, so again, you can plant the entire pot or disc.


I've had some get moldy and—like what happened when I tried to use toilet paper rolls—break down too quickly when exposed to water. I am not a fan. Plus, you have to pay for something that's not reusable.

biodegradable peat pots and trays

Seed Starting with Plastic Cups, Styrofoam Cups, and Small Reusable Pots

You can poke holes in the bottom of just about any cup and use it to start your seeds. Be sure to place them on a surface or tray that can catch runoff when you water them (like my baking sheet in my original setup).


The benefit of these is that they are bigger and thus can grow your seeds all the way to transplantation without needing to pot them up (in other words, you don't have to move them to a larger pot before they go into the garden).


The negative is that they take up way more space than the cells of a typical seed starting tray.

seed starting in plastic cups

Seed Starting with Soil Blocking

Another option that is gaining popularity is to use soil blocking. While this option has technically been around for centuries, many home gardeners have never seen it used. 


The beauty of this option is that you use the soil as both the growing medium and the container. The soil is packed enough to stay together and allow the seed to grow roots without running out of space. 


You do need a few particular items to get started.

I know many gardeners who are turning to this method and quite enjoy it. You can see the items you need here and read up on how to's.


Summer Skye Gardens

Summer Skye Gardens brings garden design and native landscape services, plus one-on-one coaching, to Spring, Texas. Their mission is to help people become confident and successful gardeners in their own backyard kitchen gardens.

Seed Starting with Plastic Trays

This is the simple and easy route, and it's what I use for the most part to start my seeds indoors. I'll list my favorite seed starting trays below.


The cells in trays are perfectly sized so that you don't have to use a lot of soil. Plus, they're reusable.


These aren't biodegradable, so you'll have to be careful removing seedlings from cells. If your plant needs more time indoors, you'll need to pot up before transplanting outside.

cells in seed starting tray

My Favorite Seed Starting Trays

My top pick would have to be from Johnny’s Selected Seeds. Everyone knows their seed starting materials are top notch, and I love supporting a company that has such a great reputation and relationship with its employees. Their trays can be a bit on the pricier side, but you know that they will last for years. They have numerous options to choose from, so here are a few you might want to try:

  • 72 Cell Plug Flat - This tray can be used for almost anything growing in your garden. These are the ones I currently use (pictured below).
  • SureRoots 50 Cell Deep Plug Flat - This tray is great for anything with a longer taproot or something that may be disturbed during transplanting, such as sweet peas or perennial plants.
  • 128 Cell Plug Flat - This tray will definitely give you plenty of spots for seeds in the space provided. This tray would work for things like greens and herbs that don’t need a ton of space.
  • Pro-Tray 24 Cell Flat - This tray with larger spaces is better for your larger plants like tomatoes, eggplant, melons, pumpkins, and squash.

With any of these trays, make sure you also order trays to catch or hold water underneath if you're growing indoors, as these trays all have holes that allow for drainage or uptake of water.

Plenty of other companies have similar tray setups that are good quality. You can get a kit from Gardeners' Supply that includes a 12- or 24-cell tray and a mat, and Burpee has a similar setup that also includes a dome lid, markers, and grow pellets. Growers Supply carries similar products, but you have to order a certain number of trays, not just one. 

Amazon has a really neat kit that has a 60-cell tray with a mat and dome lid, as well as a grow light—a great setup for beginners! You can also find inexpensive trays and kits at places like Home Depot, as well as your local gardening supply stores.

starting seeds indoors

A Couple of Quick Tips on Using Trays to Start Seeds

Tip #1

You can water at the top or the bottom. Many people get fungal disease, which affects seedling growth, by watering on top of the soil if it is kept too moist. This has never happened to me, but you want to be careful how much water you use. You can avoid this issue by pouring water into the bottom catch tray; the seedlings will absorb it up through the holes in the tray.

Tip #2

When it comes time to remove your seedlings, a butter knife is your best friend. Just insert it gently along the side of the soil and pop your seedling out.

Tip #3

Always be sure to wash and sterilize your tray kits before use for new seeds. The moment after I transplant my seedlings, I wash my trays out and remove any dirt or debris and let them dry out before storage. When it comes time to start new seeds, I soak my trays in a diluted bleach solution to kill off any lingering bacteria that could harm my new seed babies. You can use a 9:1 ratio of water to bleach, or 9 cups of water for every 1 cup of bleach.

Is a seed starting heat mat necessary? 

I personally do not use a heating mat and do just fine; however, I see plenty of gardeners and, for sure, farmers who use them and have excellent and speedier germination. I don’t feel this is necessary to get started if your space is warm, but it can definitely help.

There is also an option to purchase a dome. I have used domes at times and not used them at times, and in my opinion, they aren’t totally necessary if you have a warm space to start your seeds. If your space is a little cooler, like less than 72 degrees, then a dome can provide extra warmth and humidity for your seeds to germinate.

Learn more tips and tricks to starting your own seeds indoors

Follow along with Nicole Burke of Gardenary as she plants out her seeds in different growing containers and walks you through how to care for them, all the way until it's time to transplant seedlings outdoors. Learn how to troubleshoot common seed starting issues in this course, available with a Gardenary 365 membership.

Get Set Up for Seed Starting Success!

If this is the year you want to start growing seeds indoors, here is a complete list of items you want to have on hand, including links to my personal faves I use:

tomato seedling

And that is it! I hope this helps and motivates you to give starting your own seeds a try. It is so fun and a great way to be able to grow different kinds of plants or varieties that you can’t find at your local garden stores. There truly is nothing like picking a vegetable or cutting a flower from a plant that you started yourself by seed.

Meet the Author, Dani Boss

Dani Boss of Summer Skye Gardens

Dani Boss — Summer Skye Gardens

Dani is a Gardenary-certified garden coach and proud owner of Summer Skye Gardens in Spring, Texas. She loves giving tips for how to grow your own plants from seed or how to set up your own pollinator garden, complete with cut flowers and roses.

As a garden coach, she's passionate about helping families get started growing their own food with confidence and success in their very own backyard gardens. She offers design service, one-on-one coaching, and consultations.

Follow Summer Skye Gardens on InstagramFacebookYouTube, and Pinterest to see how Dani is helping others grow in health and happiness. If you're in the Spring area, sign up on her website to receive a free seasonal planting guide and see how Dani can help you make your kitchen garden dreams come true!

Thanks to Dani for supplying the pictures of her indoor seed starting setup for this article.


Summer Skye Gardens

Summer Skye Gardens brings garden design and native landscape services, plus one-on-one coaching, to Spring, Texas. Their mission is to help people become confident and successful gardeners in their own backyard kitchen gardens.

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The Best Seed Starting Trays to Start Seeds Indoors