Starting Flower Seeds: Perennials and Annuals

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Knowing how to start your own seeds is the best way to grow the cutting flowers you like. Starting seeds in containers lets you grow many beautiful, interesting, and less common cutting flowers for fresh and dried bouquets. Rather than trying to find those flowers at a local nursery or garden center, which most won’t have because most people don’t know enough about them, you can grow them yourself from the huge array of seeds available from many seed companies.

In this article I take you through the steps from seed to a transplantable plant and I describe my tools and methods to grow hundreds of seedlings in a compact space… without a greenhouse.

Not all plants start off well when direct seeded (sown directly into the garden soil). Many germinate and start better in containers. Some can do both. Most seed packages tell you which plants need which method. And what season to start them.

Most perennial flowers are best started in containers. I use a special container, you’ll see below, to start many seeds in a small, convenient place.

This page will help you with not only cutting flowers but also veggies and many herbs.
This is a long page but it’s full of good info…use the table of contents for quick links.

On this page

When to start seeds

You might have a greenhouse or a space indoors with adequate lighting. Many people like to start seeds early, in January, so they can start getting tomatoes in early summer. If you plant your seeds in containers indoors, the lighting must be strong enough so the seedlings don’t get leggy and weak.

I start my seeds outdoors. I don’t have a greenhouse and never have. I don’t like to start seeds indoors—I don’t want to invest in the lighting, give up the space, or deal with the mess. So I wait till later in the spring when the sun is higher, the days are longer, and the temps are warmer which help with germination and early growth. I start seeds in early April when the weather has somewhat settled, though I need to be watchful of spring hail storms and frosts.

And plenty of air circulation is healthiest for seedlings.

I use seed trays that are insulated, more on that below. But to protect against spring storms and frosts I have a covered spot to bring the planted trays to where they won’t get hit and my seedlings get damaged.

I live in the Sierra foothills in northern California, my USDA zone is 9a. If you’re in a much colder zone, you might need to set up heating mats for under the seed trays and some sort of cover like a cold frame with glass.

I usually plant my seedlings out in late May to early June.

As far as early tomatoes go, I buy a few plant starts from the many people in my area that start them early in greenhouses and sell at plant sales. But I do start some of my own favorites, I just get those tomatoes later.

Seed starting trays & containers

Container options are flats, 6-packs, peat starter trays, tiny peat pots, and other small pots. And there are soil block makers and the newspaper pot makers which use little to no plastic. And those are all good.

I like starting seeds in seed trays because it’s the most efficient use of space. You save space by getting many more seeds into about the same space as seeding into a flat, without having to transplant seedlings out of a flat into a larger container. And way more than using many small containers.

Square, cone-shaped cells in a Speedling tray — The square, cone-shaped cells in the Speedling trays

The trays have square cone-shaped cells that prevent the roots from circling, giving you nice, little plant plugs. Once the seedlings in the trays are large enough they go straight into your garden.

There are a lot of different seeding trays available. I’ve used several of them and they’re good, better than many little pots. But the seed trays I use now are made of Styrofoam. I don’t like to use Styrofoam because it’s a plastic that sheds, but I’ve had mine for 14 years now and they’re still in great condition, which I like. What’s more, the Styrofoam is a good insulator for the root zone, helping keep a steady temperature for best germination and keeping the roots from freezing. And they’re very light yet rigid, making them safe and easy to carry around when you need to move them.

The seed trays I use are called Speedling Transplant Trays. The trays are approximately 26” x 13” and come in several cell sizes. I use the trays with 200 cells and 128 cells, the 200’s being good for smaller seeds. Any cell size is good. But the large sized cells are 72 cells per tray for large seeds like gourds and squash.

I can pack hundreds of seedlings onto a 2 ft. x 6 ft. table. For a home garden flower grower, you may only need one or two 200 or 128 cell trays. More if you include your veggies and herbs.

When weather threatens my seedlings these trays are easy to move because they’re so lightweight.

You can also plant plugs out much sooner than if you planted into bigger pots, giving you a head start in the garden.

Seed starting soil

For starting seeds in a container you want a soilless mix that’s sterile and well-draining, yet holds enough water. Sterile mix will be less likely to have damping-off fungus which attacks new sprouts and kills them. You’ll know it by the way the seedlings emerge then collapse and rot.

Soilless means regular soil from the ground or your garden bed isn’t a good choice. It won’t have the drainage needed and it may have pathogens that can harm your seedlings.

Seed starting mixes are available in packages or you can make your own, which is what I do. When you use Speedling trays, you need only a little.

One problem I’ve found with packaged seed starting mix is some have larger pieces of pumice in it which interferes with fitting into seed tray cells and they need to be crushed manually, so beware.

The seeding mix is made of peat moss or coco coir and perlite or vermiculite. I give you my process below. This is only for starting seeds and growing to transplant stage. It won’t have any nutrients.

Soilless seed starting mix

For my mix I’ve been using use coconut coir made from coconut husks. I’d read quite a bit about how mining peat was destructive to the environment they come from and releases lots of carbon dioxide that was tightly held in the bogs. Therefore the coco coir made from coconut husks has been touted as more environmentally friendly.

BUT, as I was updating this page, very serendipitously I took a brief break to check my emails and found a freshly arrived trade magazine with an article questioning whether peat moss was really guilty of so much harm! It was well-researched and well-written by a scientist, and I came away convinced that peat may actually be the more environmentally friendly soil medium! A real turn-around for me. Read the article for yourself, published in Produce Growers, April 3, 2025, USDA researcher defends use of horticultural peat by USDA researcher James Altland.

But to be fair, here is an article voicing the other argument from Oregon State University, Harvesting peat moss contributes to climate change, Oregon State scientist says.And another from BHG.

So decide for yourself which to use. I have enough seed starting soil form one block of coco coir to last me a few more years. And that’s because… the Speedling trays use so little soil medium. That’s a great environmentally friendly option to me.

Coconut coir comes in compressed blocks. You can hydrate the whole thing or, if you can manage, cut off a chunk to hydrate a little at a time. But it can be difficult! If you hydrate extra you can store it. One block, once hydrated, will fill a wheelbarrow.

I put the whole block into a wheelbarrow or a metal tub, put quite a bit of water into it (it soaks up a lot!), let it sit for a few hours, then break it apart until it’s uniform and lump-free. I take out what I need and fluff up the rest sit in the sun to dry then store it in a bin.

Peat moss, on the other hand, comes in fairly loose packages and is ready to use.

Coco coir, like peat, is a medium that keeps air in the mix because of its porosity. It also holds some water. The next ingredient is one to hold a little more water and provide drainage. That can be done with either perlite or vermiculite.

Perlite provides good drainage, but holds the water all around its porous surface area. And it has a lower environmental footprint because it’s naturally produced volcanic rock. Perlite tends to cost less, too.

Vermiculite is heat expanded mica which holds water between its layers. It can contain asbestos. It holds water better, but has a higher environmental footprint because of the high heat required to heat the mica.

I choose perlite because it’s more environmentally friendly. The perlite should be a fine grade, not coarse, because the seeds are small.

That is all you need for a seed starting mix.

Next step is filling the containers

Clean your containers

Whatever containers you use they must be clean to be free of pathogens. Sterilize them by submerging them in a 10% bleach solution. An easy way to approximate that is by adding enough bleach to your tub of water so that you can smell it, but not too strongly. You may need to weigh down the containers with a brick or a rock to submerge them, especially the Styrofoam Speedling trays. Leave them for an hour or so to soak. Then rinse thoroughly.

I confess, I often skip this step for my Speedling trays. To clean them I use the jet spray on my hose-end sprayer with moderate force into each cell and all around the tray. Then I let them dry in the sun for some sterilization. I haven’t had any problems in the years that I’ve done this, but if I did, I would give everything a bleach treatment.

Filling your Containers

Fill the containers with moist soil mix, not wet or dry. When you fill your containers you want to be sure there are no large air pockets. That’s fairly straight-forward if you are using traditional pots and flats, just filling and lightly tamping with your fingers.

For the Speedling trays I spread the moist, not soaking, soil over the cells, smooth it out, and then use two fingers to tamp two cells at a time running down all the rows. Then add more soil to fill the divots.

Next I water the containers to settle the soil. Then let them dry out a little before seeding.

Planting your seeds

There’s a rule of thumb to go by. Plant a seed as deep as it is wide. But I truly believe there is a fair amount of wiggle room. So if the seed is ¼ inch wide, plant it ¼ inch deep. But don’t stress over accuracy, just come close.

In the Speedling cells I hold a seed between my forefinger and thumb, use the middle finger to push the soil away to a depth I want, place a seed or two or three, then cover it with the soil finger. This way one finger gets muddy while the other two stay dry to manipulate the seeds. Detailed, yes, but I can get a lot seeded quickly this way. You’ll figure out your best way, too.

Some seeds require light to germinate. But if I put the seeds at the surface they could get splashed out when I water them. So I put a few seeds into the cell and then push them in a bit and push a tiny bit of soil over them to help hold them. So they’re partly covered and light gets to them.

Some seeds require chilling before germination. To do this you need to mix the seeds with a slightly damp medium, like the coir, or sand. Put them into a zip-loc bag and put them in the refrigerator of 30 days, or however long is recommended. Then take them out and plant.

I have to say, I never do this. I’ve tried, but it doesn’t lend well to finding the seeds easily and putting them into my Speedling cells or anywhere but a nursery flat. So I barge ahead anyway and plant into my cells right along with everything else. I’ve never been disappointed! I think one reason is because I keep my seed trays outdoors where they are subject to the cool spring nights. I don’t use bottom heat.

So chilling is supposed to increase germination for some plants, like echinacea, but may not be entirely necessary. I think that’s true for most perennial flower seeds.

I read a long time ago from a UC Davis publication that when tomato seedlings were subjected to just above freezing night time temperatures, they fared better later in the season when cold temperatures arrived in fall. So I think there’s something to using normal (but not freezing) ambient outdoor air for growing healthy seedlings.

How many seeds to plant?

I always plant more than I’ll need. Sometimes there’s a low germination rate. Low germination can be inherent to the seed, the variety, from poor storage, or from older seed. Or from lack of chilling. To compensate, planting extra is the most time and expense efficient way to be sure you get what you want to grow. And well… those Speedling trays make it simple and space efficient, too. I also put at least two seeds in each cell, more if they’re tiny.

Label

Don’t forget to label your seeds. Trust me, you won’t remember what’s what. My system is to go from left to right and from bottom to top and put in the label in the last cell of that variety. I include the date—it’s a good reference for the next year.

Photo of seeded Speedling tray — Seeded and labeled Speedling trays

Watering your seeds

Water your newly planted seeds with a very fine spray. Otherwise the seeds can get splashed out. Fogg It Nozzles are great at being gentle, use the super fine one. Also the Dramm One Touch Spray Gun has a mist spray pattern*. Use these gentle sprayers until the seedlings have emerged and are well rooted.

Keep soil moist until germination, then allow a little drying between waterings. You may need to visit two to three times a day to water. If you’ll be away for too long, put them into more shade. It all depends on the weather.

Starting seed requires frequent watering. If they’re out in the sun, you need to watch them carefully (but it’s so fun to watch them germinate!). If no one will be at home during the day you’ll need to set up a sprinkler/misting system on a timer.

I don’t use a misting system, but I check the seeds and seedlings three times a day. If I’m going to be away for a long day I move them to the shade—which is so easy with the Speedling trays, water them well before I leave and when I get back. But only for a day max. (I’ve never had problems, except for one surprise hail storm.)

Light & Air

Give your seeds and seedlings plenty of light and air circulation. I put mine out where they get direct sunlight for at least four hours a day. Six hours is better, which is technically “full sun”. This requires regular checking for water needs. Being outside in the air gives good air circulation which is important for preventing fungal diseases like damping-off. Damping-off is a fungus that can rear its head when conditions are damp, cool, and with low air circulation.

Fertilizing

Seeds come equipped with the nutrients they need to germinate, so fertilizing isn’t needed until the first true leaves appear. (The first leaves that emerge are the cotyledon leaves; the true leaves are the ones that come after that and look like the plant’s normal leaves.)

Since the soil medium has no nutrients you now need to start supplying some. You never get the perfect scenario with all the seedlings at the same stage at the same time. So you need to make the call on when to start.

When enough seedlings are showing their true leaves, start watering with a dilute, balanced organic liquid fertilizer with minerals. I stress dilute, too much fertilizer can burn the delicate seedlings. Follow the directions on the package and go weaker in the case of young seedlings. I use MaxSea, a dissolvable balanced fertilizer with important micronutrients. Start with a weak solution and fertilize once week and increase the strength slowly until you’re ready to plant out.

Are your plants ready for planting out?

The roots of plants must fill their container well enough to hold the soil together when planting out. Too soon and the root “ball” falls apart and the roots can dry out quickly and become damaged. Check the roots of a few plant samples. They should fill the container and hold the soil together. In pots they may be circling at the bottom. In Speedling trays they will come out of the plug hole at the bottom. These roots can be trimmed off when removing from the tray and planting.

When the seedlings are ready to plant out into the garden, cut off any circling roots at the bottom…unless you use Speedling trays, then you just cut the long roots back to the bottom of the plug. But to get the plugs out of the Speedling cells you’ll need a dibble stick. Find a stick that fits into the bottom hole, but blunt so it pushes the plant plug without piercing it.

Overall try to minimize root damage. (It will happen.)

Plant into well prepared soil with a little organic fertilizer mixed into the soil. Water well.

If you have started perennial plants, some may be better off if you pot them up into a small pot, like a 4 inch pot to get larger. But healthy plugs should do well straight into the soil. I use caution and pot up a few perennials just in case something goes wrong.

Sound too complicated?

Seed starting is a bit of work and requires attention. But when you see those seeds start to pop up, it’s an exhilarating feeling, where your hopes and plans for growing fun and beautiful cut flowers start to come to fruition. And if you include plenty of perennial flowers in your seed starting process, your giving yourself easy flowers for many years to come.

Speedling tray cell with a tiny green seedling emerging — Newly emerged seedling in a Speedling tray

Starting your own seeds opens up so many possibilities to grow many pretty and unusual new flowers that are otherwise nearly impossible to find. This page should put you well on your way to growing from seeds.

Where to get Speedling trays

I got mine from Peaceful Valley Farm Supply (I live in the same town). Their online name is groworganic.com. They’re now using the same item from Hortiblock. Speedling Transplant Trays.

Greenview Aquaponics has the Speedling Rafts Transplant Trays (which is what I have.)

A few other notes:

Germination can be just a few days for some plants and up to several weeks for others. The seed package will tell you what you can expect.

You don’t always get seed germination in every container. So plan on that, be sure to plant extras. Sometimes seed is too old. Most last only 2-4 years.

When you plant more than one seed in a pot or cell you’ll end up with too many sprouts and you’ll need to remove the extras. Choose the strongest one and either pull carefully with fingers or tweezers, if they’re tiny, or clip them off with sharp scissors. Clipping them off is probably better because the roots of the remaining seedling won’t be disturbed. But I end up pulling quite a few and I’ve seen no difference.

Here’s a list of some of the plants I start in spring in containers:

Perennial flowers: perennial statice, golden yarrow, Pycnanthemum, peach-leafed campanula, craspedia, carnations, snapdragons, feverfew, Ammobium, perennial scabiosa, golden yarrow…

Annual flowers: statice, Celosia, strawflowers, amaranth, zinnias, marigolds…

Herbs: basil, parsley, lovage, Zaatar marjoram, and more…

Veggies: tomatoes, peppers, eggplants, and much more…