15 Indoor Seed Starting Mistakes You Can Prevent or Correct
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Ever planted a tray of seeds for your garden, only to have them refuse to germinate, die on you shortly after, or just fail to thrive? It’s happened to all of us at some point, newbies and seasoned seed hoarders alike.
When seedlings flop, the best thing to do is figure out what went wrong so you can either fix the problem or avoid it in the future. Hint: it doesn’t have anything to do with your thumb.
What works and what doesn’t when raising seedlings will depend on the conditions you’re working with, like most everything else in gardening. In many cases, though, seedling struggles can be traced back to some common problems with either your setup, your process, or their environment.
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Most of the seed-starting mistakes on my list come to mind because I’ve made them myself at some point. They’re all easy to prevent once you’re aware, and some can be turned around if you catch them soon enough.
1. Not Maintaining The Right Soil Temperature
Many vegetable seeds germinate best in warm soil. Some seeds, like squash and cucumbers, likely won’t germinate at all if the soil is too cold. For most things, you should aim to keep the soil around 70-75 F while you’re waiting on your seeds to sprout.
One tried and true way to encourage germination is to place your seedling trays on top of your fridge or another spot near the ceiling. Since heat rises, those places stay warmer than your room temperature. Keep in mind the majority of veggie seeds don’t need light to germinate, meaning they don’t need to be under a grow light until you see them popping up.
If your house is really chilly or drafty, you can use a seedling heat mat and/or humidity dome to help warm the soil up instead of the fridge method.
I recommend only using heat mats that are specifically made for seed starting. Regular heating pads can get way too hot, and temperatures over 90 can also hinder germination (over 100 may sterilize the seeds!). To fine-tune the temperature even more, get a seedling heat mat that comes with a thermostat and soil probe.
Once seeds have sprouted, continued high soil temps can cause leggy-ness. That means tall, floppy, weak seedlings, and you don’t want that. The general advice is to turn the heat mat off after germination to keep that from happening.
However, cold-sensitive seedlings like tomatoes and peppers will struggle even after they’ve sprouted if the soil gets too cold at their root zone. They tend to languish and turn purple (a sign of cold stress) if it drops much below 60 F.
If your growing space gets chilly at night, it’s totally fine to keep the heat mats on as long as you’re controlling the temperature with a soil probe thermostat. For my cold-sensitive seedlings, I turn the heat down to around 70 once the sprouts are all up. That isn’t enough heat to cause any leggy-ness.
2. Using the Wrong Container Size
You’d be surprised how much container size can affect the overall success of your seedlings.
Firstly, a pot that’s way too big makes it easier to accidentally overwater, since the soil takes a lot longer to dry out in the middle. You may notice it looks super dry on the top and think you need to add water, when in fact that soil is still saturated down at the plants’ root zones. Doing this repeatedly leads to root rot, damping off, and/or overall sick seedlings.
Smaller containers won’t stay in the “soggy zone” for too long. This is important for seedlings that grow and develop roots more slowly, since they’re more vulnerable to overwatering issues. Pepper seedlings have particular trouble dealing with “wet feet.”
For the above reason, I advise using smaller (2 or 3 inch) cups or cell plug trays if you’re new to starting seeds in containers. With larger pots such as solo cups, you can check the weight to tell if they need watering, but that takes practice to get a “feel” for it. Dry soil on top is a pretty reliable indicator it’s time to water, with small cells. That means less confusion and guesswork.
Smaller containers do have a few drawbacks. They’ll need watering more often, and you’ll probably need to move your seedlings into bigger pots at some point before they’re planted outside. But the benefits make it worth the hassle. It’s better to practice testing pot weight for soil dryness with older seedlings that are less sensitive to overwatering.
Pot size also factors into keeping that soil warm for the seeds/seedlings that need it. The bigger the pot, the harder it is to get cold, damp soil up to temperature for seeds that require warmth to germinate. That’s going to be the case whether you’re using a heat mat or just setting your trays in a warm spot such as on top of your fridge. Heat mats don’t do much at all with pots any deeper than 2.5 to maybe 3 inches. And again, cold, soggy soil is a recipe for seedling health issues.
3. Using the Wrong Planting Mix
What you fill your pots with is just as important as the pots. Seedlings grown indoors do best in soilless mixes meant specifically for seed-starting, not soil from your garden or regular potting mix.
Garden soil may be harboring disease organisms that can run rampant in an indoor setup (not to mention insect pest eggs). Regular potting mix tends to be heavy, so it may not drain well enough to keep seedlings’ roots from getting water-logged. Also, potting mixes that aren’t all natural often come with added synthetic fertilizers that could burn tender sprouts.
Seed-starting mix is inexpensive to buy in small bags, or you could opt to follow a DIY recipe and make your own.
If you buy your mix from the store, it’s a good idea to inspect it before you sow your seeds. It should be soft and fluffy and should not be loaded with wood or bark (finding a few little pieces is fine, though). Sometimes, soil companies try to stretch their inventory by adding fillers like raw, green wood or bark chips and calling it “compost.” I’ve seen that with both seed starter and potting mixes in the last couple years.
4. Not Wetting the Planting Mix Before Sowing
Your seed starting mix should be pre-moistened before you fill containers and sow seeds. Otherwise, the mix will shrink down a lot the first time you water your trays, and you’ll find your containers are only 2/3 full. Plus, watering dry mix is more likely to displace your seeds.
To pre-moisten your seed starting mix, dump what you think you’ll need in a large bowl or bucket. Then, add in water until you can take a handful and squeeze out a tiny bit of moisture between your fingers. While you don’t want it to be sopping wet, slightly over-moist is better than too dry.
5. Leaving Air Pockets in the Planting Mix
I’ve read a lot of seed-starting guides say you should never pack the seed-starting mix into your containers. And they’re right, it shouldn’t be compacted. But these mixes tend to be so light and stringy they form big air pockets if you just scoop it in and call it done. You don’t want that open space around your seedling roots. Plus, if a seed is not fully in contact with the damp soil, it will dry out and may not sprout.
You can avoid the above problems by carefully tamping down the soil surface with a fingertip after filling the containers, just enough to close any gaps. Then, top them off with more soil if needed. Giving the trays a good, heavy misting with a spray bottle after sowing the seeds will also help settle things in.
Bad planting mix is another usual culprit in poor seed to soil contact and poor germination. If the mix is too coarse, the big pieces of stuff in it will create gaps around tiny seeds. It needs to be finely textured so it gives the seeds a tight hug.
6. Not Planting at the Correct Depth
Getting the planting depth wrong will slash germination rates. Some seeds, such as dill, need light to sprout and must be surface sown. Others need complete darkness. If these conditions aren’t met, you’ll get little to no sprouts. Check the back of your seed packets for info about planting depth.
Unless you’re even more of a perfectionist than me, you’ll probably be guestimating at the depth when you sow your seeds. In most cases, it’s a good idea to err on the shallow side. I like to use a knife to make a little furrow, drop the seeds in, and gently scrape the dirt back over them. This method makes it easier to see how deep you’ve actually put them, as opposed to just pushing them into the soil with your fingers.
7. Planting Seeds Too Late or Too Early
If you sow your seeds too late, the seedlings will be too small to plant outside when conditions are right. This might be a big problem in zones with short growing seasons, since your plants may not have time to produce a harvest before the first fall frost.
If you sow too early, you’ll have seedlings outgrowing their starter pots when it’s still too cold to put them out. The three-hour process of potting up dozens of seedlings a second time is especially frustrating knowing it could’ve been avoided, if you’d just waited two more weeks to start!
Read this post for tips on creating a seed-starting schedule that works smoothly for your garden: Timing Indoor Seed Starting: When to Sow Seeds for Your Spring Garden.
8. Not Using Grow Lights
Putting seedling trays next to a window instead of using a grow light is how you get leggy seedlings. New sprouts want the light directly above them; if it isn’t, they’ll stretch towards it until they get thin and floppy. Leggy seedlings grow up to be flimsy plants that are more vulnerable to damage from wind and rain.
Grow lights are a must if you’re serious about raising seedlings inside, but you don’t need to spend a fortune on them. Cheap grow lights will work just fine for getting your seedlings to transplant size.
9. Keeping Grow Lights Too Far Away
I’ve found that the recommended distance on the product instructions is never close enough, with cheaper LED grow lights. They’ll usually say you should keep the light 12 inches or more above the seedlings, but these low-budget lights are often not bright enough to be effective from that far away.
When the lights aren’t close enough, seedlings will get pale and leggy. I usually hang my lights about 4-6 inches above the tops of the plants. These wire racks I bought for my seed starting trays make it easy to hang bar-style grow lights and adjust their position as the seedlings grow.
Of course, the right distance is going to vary between different kinds of lights. If the bulb on your grow light feels hot to the touch, start by hanging it according to the directions. Then, keep a close eye on your sprouts. You’ll know it needs to be closer, if they start to look a little tall. Slightly leggy seedlings will be just fine, as long as the problem is caught and fixed in time.
If your light feels cool or only slightly warm to the touch after being on for a while, it’s a safe bet to start by putting it six inches above the seedlings, moving it closer if necessary.
Higher-powered grow lights can burn seedlings if they’re too close. Lights like this are usually expensive and are intended for growing plants to maturity indoors. I’ve never had this happen with my budget LED grow lights, and I’ve accidentally let the tops of the seedlings touch the bulbs when they hit a growth spurt (more than once. Oops).
Grow light tip: sometimes, the cheaper LED grow lights don’t have super even coverage. If that’s the case, you might need to shuffle your seedlings around once a day so they all get even lighting. No biggie. You’ll know to do this if the seedlings on the edge of the tray start to stretch inward.
10. Overcomplicating Watering
You’ve probably heard of the Goldilocks principle for watering seedlings. They don’t like their soil too wet, and they don’t like it too dry. It has to be just right. It’s easy to overthink, and ironically, overthinking it can lead to over or underwatering. The key is to try and water only once the soil looks and feels dry on top.
Here’s what you need to know about overwatering: it doesn’t happen from occasionally watering soil that isn’t quite dry enough yet. It also doesn’t happen from watering too much at once. Over-watering happens when you repeatedly drench soil that is still saturated, without allowing it to dry out some in between.
One of the easiest ways to overwater your seedlings is trying to water on a fixed schedule instead of letting the soil tell you when. The mix will dry out at different rates based on temperature and humidity, and those conditions change with the weather (even inside your house). If you go to water and your seedlings’ soil is still dark and wet to the touch, wait until later.
For more help with watering seedlings, see this post: How to Properly Water Your Indoor Seedlings.
11. Not Removing Humidity Domes After Germination
Seed-starting kits often come with humidity domes, which fit over seedling trays like a lid to create a greenhouse effect. They hold in moisture and heat to help your seeds germinate faster, but they can cause trouble if used wrong.
Even with the little vent holes open, the ongoing high moisture and low breathability environment under the dome can lead to mold growth. Worse, it creates the right conditions for damping off (a deadly seedling fungal disease) to develop. To prevent issues, a humidity dome should be removed immediately after the first sprout has broken the soil. Humidity domes also block the grow lights quite a bit, and the seedlings will quickly get pale and leggy if the dome isn’t removed in time.
I rarely use domes because my grow room stays pretty humid as is. If your seed-starting area has lower humidity, you might have good results with them. Just don’t be tempted to leave it on too long. If you see one sprout, the others are probably awake, too. They just haven’t poked their heads out yet.
12. Not Thinning Seedlings Properly
Sometimes, you might want to sow two or three seeds per cell instead of just one. This is called over-seeding, and the point is to make sure you don’t have any gaps in your trays if some of your seeds don’t germinate. Once your seedlings are growing, you’ll need to thin them down to one seedling per cell. Otherwise, you’ll have overcrowded seedlings trying to share limited water and nutrients, which will affect their health and growth.
The two main pitfalls here are 1) not thinning at all, and 2) trying to remove and re-pot the extra seedlings instead of snipping them off.
While it might sound silly to some folks, I completely understand getting emotionally attached to seedlings. It feels heartless to terminate any of your little babies. But if you try to separate and re-plant them, you risk damaging the roots of the seedlings you’re not thinning. Seedling roots are fragile, so it doesn’t take much. Your best bet is to leave the strongest seedling in each cell and carefully snip the others off at the soil line with a pair of sharp scissors.
Thinning should be done once the seedlings are developing their first true leaves. At this point, you should be able to tell which ones are the biggest and strongest.
13. Not Potting Up
Not all seedlings will have to be potted up before moving to their permanent spot outside, but the ones that do need it will struggle if you don’t. If you’re planting in small (3 inch or less) cell trays, anything that has to stay inside for more than a couple weeks is going to need a bigger pot before it’s over.
Re-potting is typically recommended when the seedling has developed a second set of true leaves, but it’s best to just let the plant tell you when. Roots poking from the drainage holes is a good sign you need to check. If you slide the soil out of the container, are the roots looking dense and starting to accumulate around the bottom? That means it’s time for a bigger pot.
Seedlings that aren’t repotted as needed will end up root bound, which happens when the roots begin to wind themselves into a thick mat along the inside of the pot. Root bound plants always get in a funk and have trouble establishing once they’re planted in the ground.
14. Not Fertilizing When True Leaves Come In
Seed starter mixes contain little to no nutrients, so most seedlings do best with an appropriate feeding regimen. Unless I plan to transplant them out within a few days, I start feeding mine with a water-soluble fertilizer as soon as they have a fully formed set of true leaves.
Sure, they’ll probably still be alive at planting time even if you don’t do this. But you’ll be amazed at the difference it makes in the health of your transplants. Here’s some more info about using fertilizer for potted seedlings: How to Fertilize Seedlings (and Why You Should)
15. Not Hardening Off for Long Enough
Hardening off is the process of gradually acclimating indoor-raised seedlings to outside conditions before you plant them in ground. It’s tempting to rush this, because it’s annoying to carry seedling trays in and out. And in. And out. And in. And out. But the more time you spend on it, the more resilient your seedlings will be after transplanting.
Seedlings that aren’t hardened off slowly enough will experience transplant shock and languish for several weeks. Usually, they can be nursed through with some extra TLC, but it’s a setback you’d rather prevent.
Plan to spend at least two weeks hardening off. More is better, because real sunlight provides a great boost for seedlings as they get older. My indoor seedlings start getting their first sunbathing sessions around a month before their moving date.
Sun scorch, heat stress, or shock from colder temperatures are the biggest threats to your seedlings when you begin taking them outside. They should be introduced to these conditions in small increments, starting with an hour and then adding another hour each time they go out. Read this to learn more about hardening off your seedlings: How to Harden Off Seedlings The Right Way (and Prevent Transplant Shock!)
Final Thoughts- Record Your Results, and Don’t Be Discouraged
One of the best things you can do to improve your success with raising seedlings is to keep a garden journal. Write down the dates you sowed each seed variety, what did well and what didn’t, what solved a problem, etc. It’s easier than you’d think to forget the details by the next year. Keeping record helps you fine tune your sowing dates and pin down the strategies that work best for you.
Plants are resilient, determined things. If your seedlings are struggling for one of the post-germination reasons I mentioned, they’ll outgrow that kind of setback surprisingly fast once their needs are met. Just remember you aren’t taking a huge loss if something goes wrong to the point it isn’t salvageable. Seeds are cheap, and you’re learning stuff!
