Shopping For the Best Seed Starting Trays: My Top Picks

For us gardeners, starting seeds indoors is exciting, rewarding, thrifty, and offers the most variety in plants we can grow. The most crucial piece of equipment needed for seed starting is something to plant in.

Whether you use cell packs, soil blocking, a humidity dome, Jiffy peat pellets, trays for bulk sowing, or solo cups, it is incredibly important to use the right seed starting container at the right time. So, with all the options out there, how do you choose what’s best?

This blog post is here to help you select seed starting trays you’ll love. Plus, you'll learn what I use in my retail greenhouse so you can start seeds like a pro!

My Top Picks 

I love sharing gardening hacks, stories and lessons from the garden, and top-notch gardening advice with people so that they can Grow Bigger! From revealing my grow room setup and my search for the best greenhouse kits to tutorials on using grow lights, seedling heat mats, and grow bags, I hope you’ll use MIgardener’s free resources to grow your best garden yet.

If you want to cut to the chase and are ready to buy great seed starting trays without any further information, here’s a spoiler: these are my favorite seed starting trays that I use year after year:

• 128 Cell Plug Tray

• 72 Cell Seed Starting Tray

• 6 Cell Tray Inserts

• 4 Cell Tray Inserts

• 1020 Extra Strength Trays (With or Without Holes)

• 1020 Shallow Tray

• 2.5” Heavy Duty Seed Starting Pots

• 3.3” Heavy Duty Seed Starting Pots

Best Seed Starting Trays for Flowers & Vegetables

In my opinion, the highest-quality seed starting trays on the market are made by Bootstrap Farmer. I use Bootstrap Farmer for all of my seed starting supplies because they are top-quality, made of BPA-free food-safe plastic, made in the USA, and built to withstand any growing environment. 

These are not your typical throw-away seed trays, but last for many years of continued use! They are made for the gardener who wants a heavy-duty, reusable option. 

Understanding Cell Size in Seed Trays

When you start shopping for seed starting trays, you will find they come in all kinds of sizes, dimensions, and cell counts. A higher cell count in a tray means each individual cell will be smaller. For example, a 72-cell tray has larger individual cells than a 128-cell tray.

Choosing the wrong size seed starting cells or pots is a common mistake. Too small means that the root system and leaves of the seedling will outsize their growing space right from the start.

When the starting pot is too large, root development is inferior, growth is far less vigorous, and seedlings are more prone to damping off and root rot. Many growers make this mistake, hoping they won’t have to transplant as often, but it will cost them later! 

128 Cell Tray

I find that 128-cell trays are ideal for small seeds that grow relatively quickly and don’t need much time indoors. It's best to use a 128-cell plug tray for flowers, herbs, lettuce, and brassicas (cabbage, kale, cauliflower, mustard, broccoli, watercress, etc.). 

The Bootstrap Farmer 128-cell plug tray is slightly wider at the top and tapers to the bottom for easier plant removal. It extends to the bottom of a standard 1020 seed starting tray, so you can effectively bottom-water your seedlings.

72 Cell Tray

A 72-cell tray can also be used for flowers, herbs, lettuce, and brassicas, giving them a little more grow time before they need to be potted up. You can additionally grow crops like tomatoes and peppers in this size tray.

The Bootstrap Farmer Extra Strength 72-cell Plug Seed Starting Tray will nest perfectly in a 1020 seed starting tray. Its individual cell dimensions are 1½” square by 2¼” deep.

6 Cell Tray Inserts

Six-cell trays are great for growers who are starting a wide variety of crops and flowers. Twelve of these removable inserts fit into a 1020 seed starting tray.

In the Bootstrap Farmer 6 Cell Tray Inserts, each cell measures 1 1/2" x 1 1/2" on top, tapering down to 1" at the bottom. They are built to last many years and feature “Air Prune technology” with air channels on each side to prevent root circling. (Air-pruned roots show healthier, more vigorous growth!) 

4 Cell Tray Inserts

Four-cell plug inserts are a little larger and deeper for starting varieties of crops that need more room. They are also perfect for potting up plants like peppers, tomatoes, and flowers. Eight of these removable inserts fit into a 1020 seed starting tray. 

In the Bootstrap Farmer 4 cell plug tray inserts, each cell measures 2 3/8" x 2 3/8" on top, which tapers down to 1 1/4" at the bottom. Like the 6-cell tray inserts, the Bootstrap Farmer 4-cell inserts also feature Air Prune technology.

Seed Starting Pots

Seed starting pots are commonly used for starting large seeds, like pumpkins, or for potting up seedlings into larger containers before they can be moved outdoors. Potting up seedlings helps ensure they can grow their roots freely and develop to their full potential.

Bootstrap Farmer carries 2.5” Heavy-Duty Seed Starting Pots and 3.3” Heavy-Duty Seed Starting Pots, both of which are designed to fit perfectly in a 1020 seed starting tray.

If you are still not sure what size seed starting container you need, the video at the beginning of this blog post will help you choose the right container for the plants you are starting.

Shallow Trays

Seed starting trays are commonly referred to as flats or 1020 trays in the greenhouse industry. You may even hear them called propagation trays. Whatever you call them, 1020 trays are essential for holding cell tray inserts, but that’s not all they’re good for! 

Shallow flats are versatile and perfect for growing microgreens or planting seedlings in bulk. Unlike flimsy planting trays from the big box store, Bootstrap Farmer 1020 shallow trays don’t easily bend or break, dumping your beautiful plants on the grow room floor!  

Deep Seed Starting Trays

Deep seed starting trays are also multi-use. They are perfect for holding cell tray inserts, fodder and fodder systems, growing microgreens or wheatgrass, and hydroponics. In the blog post What to Plant in February, I show how to start root crops like ginger, sweet potatoes, and turmeric in deep seed starting trays!

Bootstrap Farmer 1020 deep trays can be purchased with or without drainage holes. They are designed for repeated use and abuse. We have tested these propagation trays with over 50 lbs. of weight without breaking!

The Shape of the Seed Starting Container is Important

Believe it or not, the shape of the container makes a huge difference in the overall health and development of the root system of seedlings! The best shape for seed starting is a square cell.

Roots grow out until they hit a barrier or air. In a circular pot, they hit a curved barrier, bend and continue to grow. The roots continue to bend and basically wrap around a lot of times, and that's when you get a rootbound or potbound plant. 

In a square container, the roots will grow out, hit a barrier, then turn and hit another barrier, essentially moving inward and outward rather than around and around. A hexagon-shaped cell is closer to a round shape, but still superior because it has edges and corners.

For years, I started seeds in solo cups with holes poked in the bottom. They’re inexpensive, disposable, and easy to use. They worked great for the first couple of weeks, but after that, problems like coiling roots would start.

If you really want to take your gardening game to the next level, change the shape of your seed starting containers to a square.

When to Pot Up Seedlings Into Larger Cells

When a seedling outgrows its original seed starting container, its time for transplanting to a larger pot or planting it outside. I’ve already dedicated a blog post to how to identify when its the right time for transplanting so you can avoid stunted plants that fail to thrive.

And one final note, don’t forget to properly harden off seedlings before you transplant them into the garden!