Selecting the Right Seed Starting Cell Trays | Bootstrap Farmer

05 Jun.,2025

 

Selecting the Right Seed Starting Cell Trays | Bootstrap Farmer

WHAT PROPAGATION TRAY IS BEST FOR YOU?

The best size cell plug seed trays for you to choose will be dependent on a few factors. We will go over the different options to help you select the best for you. Consider first, what is your intent in seed starting?

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What size cell tray should I use?

Quickly review some of these seed starting questions.

  • Are you growing a large number of one variety of plants for transplanting row crops?
  • Are you planting smaller numbers of a wide variety of plants?
  • Will you be planting your crops all at once, or will you be using the succession planting method?
  • What type of seeds will you be planting? Peppers, tomatoes, lettuce, watermelon, etc.? 
  • How large are the seeds?
  • How long will your seedlings need to stay in the cell trays?
  • Will you be potting up your plant starts or planting out directly from the plug trays?
  • How much protected growing space do you have to start seeds in?
  • Will you use a heat mat or rely on ambient temperatures for germination?

Check out The Ultimate Growing Tray Guide video for a look at how these trays are commonly used.

Seed Starting Trays Comparison

What size cell seed trays should I use for a Home Garden?

4 Cell Seed Starting Trays

Our brand new larger 4-cell plug inserts are deeper for growing varieties of crops that need a little more room. Eight of these removable inserts fit in a Bootstrap Farmer .

6 Cell Seed Starting Trays

Our  6 cell trays have large 5/8 inch drainage holes on the bottom making it easy to remove your plant starts. They also make use of air pruning technology with long vertical slits on all 4 sides to prevent root circling in your seedlings. For easy color coding and tracking or your starts we are super excited to also offer our 6-cell trays in 5 cheerful colors. These are great for gardeners who will be starting a small amount of lots of different varieties as you can remove each type as it is ready without disturbing all the other starts that are sharing its heavy-duty deep tray  bottom watering tray. 12 fit in each tray or 6 to a tray. 

Shop Bundles & Kits here.

32 Cell Seed Starting Trays

The 32 cell plug propagation tray inserts are the largest cell seed starting tray size that Bootstrap Farmer carries, measuring 2" x 2". The larger size makes them perfect for canopy development of crops. You can also use this size as an insert tray to hold our 2.5" seed starting pots.

These cell seed tray inserts can be used in two ways. Directly plant into these cell inserts with deep drainage holes with Rockwool cubes, soilless media, or soil mediums. The entire tray can be bottom watered using a  shallow tray with no holes

Another way these insert trays are used is as a holder for these seed-starting pots. Seamlessly designed to sit in a shallow tray with no holes, the insert will hold 32 of these  2.5" pots, keeping them from tipping over in a trays and making quick work of transporting them out to the garden space. The individual seed cup style is very popular for school and community projects as these can go from seed to transplant without needing up-potting in between and come in bright colors and now in clear!

Recommended Plants:  Tomatoes, Melons, Cucumbers, Pumpkins, Squash, Peppers and other large-seeded crops

50 Cell Seed Starter Trays

These 50 cell propagation trays are a happy medium of saving you space in your seed starting area while still being able to plant a large number of seedlings like lettuce that will be directly transplanted. Because the 50 cell tray has a much larger soil volume than the 72 cell plug trays or 128 cell trays, you will have a bit more wiggle room when you need to transplant for optimal root growth. Plants grown in these trays will be less likely to become root-bound if unsettled Spring weather delays your planting. This size also allows for canopy development of the seedling.

If you know that your seedlings will need to be potted up before they are ready to move outside, you will want to select one of the cell trays listed below or plan on potting up into larger pots like our new 5 inch grow pots with carrier. 

Plastic trays of this size are great for planting early greens and brassica crops like broccoli and collard greens for the home garden. Just be sure that if you choose to mix varieties in one cell tray, they all have similar germination times and time to transplant. 

Recommended Plants: Lettuce, brassicas, cucumbers, slow-growing flowers, and herbs.

The Best Cell Plug Tray Size for Large Scale Market Gardens

72 Cell Plug Seedling Trays & 72 Cell Air Prune Trays

The 72 Cell trays are the most popular choice amongst market gardeners. They are a good balance between space for growing and seedlings per tray. Each cell is 1.5" square and 2.25" deep, making them an excellent option for a large variety of plants. These plastic trays are also a good choice for vine plants. However, you will want to transplant the vine plants earlier than you would with the 32 Cell trays to prevent root bound seedlings. This cell plug tray is designed to use a heavy-duty  deep tray for easy bottom-watering.

For optimal air pruning and extremely happy plants, we recommend our 72 air prune trays. All the benefits of soil blocking without the mess! 

Recommended Plants: Sunflowers, Early Season Peppers, Early Season Vine Crops, Early Season Cole Crops (Cabbage, Cauliflower, Collards, Kale, Mustard, Kohlrabi, Broccoli, Brussels sprout, Watercress)

128 CELL TRAYS

These 128 Cell Trays are a great choice if you wish to start row crops or many baby greens. This configuration is ideal for starting many seeds but is not meant for crops that need more than a few weeks. Each cell is 1" square and 2.25" deep. You will be able to plant 78% more seedlings with one tray than the more common 72 cell seed starter trays. These 128 seed trays are compatible with the heavy-duty deep tray for bottom watering. You will want to up-pot your seedlings from this size seed tray into a larger pot or grow bag if you do not plan to transplant outdoors for an extended period to prevent seedlings from becoming root-bound.

Recommended Plants: Lettuce, Herbs, Cole Crops (Cabbage, Cauliflower, Collards, Kale, Mustard, Kohlrabi, Broccoli, Brussels sprout, Watercress), Celery, Leeks, Flowers.

The company is the world’s best cheap seed starting trays supplier. We are your one-stop shop for all needs. Our staff are highly-specialized and will help you find the product you need.

200 CELL TRAYS

These 200 Cell Trays are excellent trays if you want to be economical about growing cole crops, lettuces, and other small-seeded crops. You will be able to grow ~2.8 times as many plants with one tray as you would with a 72 cell tray. Each cell is 0.75" square and 2.25" deep. 

If you are using a 200 cell plastic trays to start seeds, you will need to transplant your seedlings at an earlier stage. Typically once they have one, at most two sets of true leaves. This plastic tray size is most frequently used by larger-scale farmers and those who intend to pot up their seedlings multiple times before moving outside. They can also be used to start plants going into hydroponic systems if you use a soilless media like coco coir or ProMix.    

Recommended Plants: Lettuce and Brassica Crops (Cabbage, Cauliflower, Collards, Kale, Mustard, Kohlrabi, Broccoli, Brussels sprouts, Watercress), Small seeded flowers. 

Common Questions About Planting in Cell Trays

Can I plant root crops in plug trays?

While some experienced farmers have successfully planted crops like beets and turnips in cell seed trays, it is not recommended unless your climate does not allow for the direct seeding of root crops. Carrots, parsnips, turnips, and beets rely heavily on their taproot. This long central root is responsible for much of the water uptake of these plants, and if the root is disturbed or damaged during the transplanting process, the plant will not thrive. 

Can onions and leeks be planted in seed starting trays?

Yes, unlike other root crops, members of the allium family have congregate root structures. This means that they are much more tolerant of root disturbances during transplanting. It is common for growers to plant multiple small seeds per cell and tease them apart for later transplanting.   

What are the advantages to starting seeds in cell trays vs. larger pots?

Starting seeds in cell trays, especially in the larger ones, gives the grower the advantage of being able to start more seedlings in their growing space. This is especially handy for row crops where the grower may want to plant 100 or more of each variety. Growing this many seedling starts in larger seed pots would take up way too much space. The other advantage is that you will waste less growing media starting out your seeds and then up-potting the successfully germinated starts into new pots. 

Can you overwater seedlings in cell seed trays?

Yes. It is possible to overwater seedlings growing in cell trays. A common mistake growers make is to leave water in the bottom tray at all times. This will eliminate your seedling’s ability to get oxygen. Bottom-watering with a can be properly done by adding just enough water to allow the cell tray to evenly absorb it during the watering and no more. You want to discard the excess water as it will become stagnant and invite anaerobic bacteria to wreak havoc on your newly established seedlings. 

Related: Easiest Way to Water Seedlings

How long can my plants stay in the cell tray?

Most seedlings can stay in cell trays for at least 4 weeks. The larger the cell volume, the longer a plant can grow before it becomes root-bound. Plants grown in a 200 cell tray will typically need to be potted up or transplanted outside once they have a full set of true leaves. Plants grown in a 32-cell insert pot can be kept in protected conditions for 6-8 weeks. Check out our 3.3" seed starting pots and 5" pots for up-potting starts or shop our seed starting bundles.

Why are my transplants not growing?

If your seedlings have been in the plug tray for too long, they may become root-bound. If this happens, you will see a large number of roots circling the plug when you pull it out of the tray. Plants that have become root bound do not produce new roots easily and will often stay stunted.

Transplant shock can also cause your garden plants to be stunted and remain small throughout the growing season. For more on how to avoid transplant shock, check out our Seed Starting 101 Guide for advice on how to harden off your transplants. 

Can I fix a root-bound seedling or plant?

If your seedlings become root bound before you have time to plant them, you can improve their chances with a bit of extra work at planting time. Once you have the plug removed from the cell tray, gently tap the bottom of the roots to loosen the soil and use your fingers to tease them apart. It is ok and even desirable to tear a few of the roots when you do this. Separating and tearing the roots will encourage the transplant to produce new side roots and prevent further root circling. 

9 Essential Steps for Starting Seeds Indoors Successfully

Starting seeds indoors is a time-honored way to get a jump on the growing season. And with just a few dollars-worth of seeds, you can grow lots of plants very inexpensively. Starting your own seeds also allows you to try out unusual and interesting varieties that you can't find at a local garden center. Here's what you need to know to successfully start seeds indoors for planting in your garden once temperatures warm up in spring.

When to Start Seeds Indoors

Exactly when to start your seeds depends on your climate and the types of seeds you're growing. Look on the seed package label to find the number of weeks suggested to start the seeds indoors before the average last frost date for your area. It usually takes about six to eight weeks to give your seedlings a good head start on spring, so count backward from your area's frost date to figure out when you should start your seeds indoors.

Steps for Starting Seeds Indoors

Once you've figured out when to start your seeds, follow these steps to plant veggie, herb, and flower seeds indoors in pots.

1. Gather supplies.

Even though the planting instructions on the packet might vary, you'll need the same supplies to start any seeds indoors. Here's what you'll need:

  • Seed-starting pots with drainage holes (or DIY seed starting pots)
  • Seed-starting mix
  • Labels

2. Fill pots.

Fill pots with fresh, moistened seed-starting mix. Don't use garden soil, which is too heavy and may have insects or diseases in it. Leave about a quarter-inch of room at the top to make watering easier.

3. Sow seeds.

Follow the seed packet instructions for planting. Some will suggest making a shallow hole in the center of the potting mix to put the seeds in and others will say to add seed right on the surface. Add one seed to each pot or cell for large seeds, and 2-3 for smaller seeds. Use the crease of the seed packet or place seeds in a creased piece of paper to help direct the seeds where you want them to go.

4. Add water.

Once you've sown the seeds, mist each container enough so that the potting mix is damp, but not drenched with water. The water will also help the potting mix settle around the seeds.

5. Label and cover seeds.

Label each of your pots so you know what's growing in them. Loosely cover the pots with clear plastic wrap or zip-top bag, which helps maintain humidity and warmth around the seeds.

6. Keep pots warm and watered.

Place your seed pots in a location that's warm and free of drafts, but not in direct sun. The ideal temperature is about 75°F but no hotter than 90°F. Once the tiny seedlings emerge, remove the cover and move them into a sunny window or under grow lights as necessary. They need about 12 hours of light a day to grow properly.

7. Thin out seedlings.

As the seedlings make their presence known, they need more space. Keep the ones that look healthy and strong, and snip the rest so there's just a single plant per pot.

8. Repot seedlings.

After they're about two inches tall and have a couple sets of leaves, your seedlings need an upgrade. Transplant them into larger containers, this time in regular potting mix instead of seed-starting mix.

9. Harden off seedlings.

Before moving your seedlings out into the garden (keeping your frost-free date in mind), you need to give them a few days to get used to life on the outside. That's what's known as hardening off your plants. To do this, place the seedlings outside for a short time in a protected spot (about an hour or two). Each day, increase the length of time you leave them outside until they can remain outdoors all day.

If you are looking for more details, kindly visit Seedling Trays Price.

Best Seeds to Start Indoors