Purple Leaves and Stems on Tomato Seedlings – Cause & Fix


This post contains affiliate links. As an Amazon Associate TinyGardenHabit.com earns from qualifying purchases.

Ever since I switched to growing tomato seedlings indoors, under grow lights, I’ve noticed something strange happen to my tomato seedlings: they’re often turning purple. This has happened to my tomato seedlings at various stages of their growth, and even though it didn’t have serious consequences, it made me want to investigate.

You’ve probably learned by now that tomato plants are fickle creatures. When they experience stress, they like to show it – either with tomato leaf curl, or in our seedlings’ case – turning purple.

Tomato seedlings may experience purple stems or leaves turning purple when they’re in need of fertilizing or suffering from various stress factors. The most common causes of purple tomato seedlings are phosphorus or magnesium deficiencies, cold soil temperatures, or grow lights that are too strong.

Not all purple tomato seedlings look the same or are affected by this problem at the same stage. Here are some common examples of what you might be experiencing:

  • Purple stems on young tomato leaves that don’t yet have true leaves.
    This is very common and they usually recover as they grow. Do nothing for now, as it’s too soon for fertilizing.
  • Purple bottom leaves, sometimes purple stems and suckers on older tomato seedlings.
    Bottom leaves going purple is often a sign of phosphorous deficiency, which we’ll soon cover. Fertilize as instructed below and keep an eye on new growth.
  • Purple veins on the back of tomato seedling leaves.
    The top of the tomato seedling leaves may look normal and green, but the backs of the leaves are a darker purple color. This is also an indication of nutrient issues. If your plant is older than 2 weeks, you should consider fertilizing.
  • Purple, rolled up leaves on your older tomato seedlings.
    Many factors can trigger leaf curl on your tomato seedlings, and when coupled with a purple tint, it becomes obvious that the plant is stressed. If you’ve been fertilizing, other culprits could be cold temperatures, overwatering, light issues, or all of the above. I’ve had this problem and it’s hard to identify the exact cause.
  • New growth on top of the tomato seedling is purple or a darker color.
    If your tomato seedlings have grown tall enough to reach the growing lights, they might be sunburnt. Some lights are very intense, and not only do the seedlings grow faster, but they can also develop a purple tinge.

How do you fix purple tomato seedlings?

First of all, don’t panic. This is a common issue and it rarely stunts the growth of your plants. As soon as you can transplant your tomato seedlings outside, they should fully recover and grow new leaves and stems that are green and healthy.

If you’re dealing with purple tomato seedlings and you’re not sure of the cause, try eliminating them one by one, starting with fertilizing. Remember, you should only start fertilizing your tomato seedlings once they’ve grown two sets of leaves, and even then, use the fertilizer at half strength.

Know what’s in your starting mix before using it – some starting mixes like pure coco coir or peat starting mix don’t have any nutrients in them, while others have added nutrients. You may have your own recipe with added compost or fertilizer – I like to mix coco coir with vermicompost and perlite (or sand). If your starting mix recipe already contains fertilizer, it’s best to delay feeding your tomato seedlings.

Phosphorous deficiency

Tomato seedlings with a phosphorous deficiency often have stems and bottom leaves going purple. If you suspect phosphorous to be the cause of this, you can try feeding your seedlings.

You don’t need to feed your tomatoes pure phosphorous. Instead, choose a general fertilizer with a good NPK ratio. See that your fertilizer has a higher percentage of phosphorous and a lower ratio of nitrogen.

There are a lot of synthetic fertilizers out there, but if you’re looking for something more natural, fish and seaweed fertilizers are a fantastic organic option for feeding your tomato seedlings and tomato mature plants. I like to use them because they’re in liquid form and you just mix them with water – easy and convenient!

Here’s an all-purpose fish fertilizer that works well at the seedling stage, but be careful not to overdo it. Later on, try a Tomato & Veg formula that’s designed for mature tomato plants – you can start applying it as soon as transplanting your tomatoes outside. Fertilize every 2 weeks for best results.

With any fertilizers you use during the seedling stage, make sure to dilute them at half strength until they are about 8-10 inches tall, after which you can switch to a full-strength fertilizer. It’s always better to underfertilize your tomato seedlings, as overfertilizing does more damage than good.

Magnesium deficiency

Magnesium is a crucial nutrient that is involved in chlorophyll production. When lacking, leaves can show a purple or brown tint. To make sure your tomato seedlings have enough magnesium, you can treat them with a foliar feed. Foliar feeding simply means you spray the leaves with a liquid fertilizer. Here’s how to do it:

Mix half a spoon of Epsom salt with a gallon of water (this will create a half-strength feed) and fill a spray bottle with your Epsom salt solution. Use it as a foliar feed on the leaves of your tomato seedlings.

You can use this half-strength foliar feed in conjunction with the phosphorous feed described above – once every two weeks. Once your seedlings are potted on and taller than 10 inches, you can switch to full strength for both feeds.

The soil is too cold

Cold temperatures can severely stunt the growth of your tomato seedlings, as they don’t tolerate temperatures below 50°F (10°C). Cold soil can also cause phosphorous to be less available for root absorption and you end up with purple tomato seedlings.

It can be harder to control the temperature of your growing environment if you’ve started your seedlings in a greenhouse or a cold frame. If you have access to a heater, set your thermostat at 50°F(10°C) during the night to make sure you don’t shock your seedlings. Also, try not to start your seedlings too early, until you reach more favorable temperatures.

If you have access to a hotbed, it’s an excellent way to keep constant heat under your tropical seedlings, like tomatoes and peppers, but you can get the same result with heat mats.

You can find various heat mats on Amazon.com, I use this specific size to warm all my tropical seedlings (tomato, pepper, chili and aubergine seedlings), but I’ve given up on using a thermostat since I don’t feel like they’re accurate anyway.

Growing tomato seedlings indoors helps to better control the temperature and growing conditions, but not always (especially if you’re growing seedlings in a cold garage or basement). Do your best to make it warm and cozy for your tomato seedlings – the sweet spot is between 65°F(18°C) and 80°F(26°C).

If your room or greenhouse is rather cold, make sure not to overwater. Watering your seedlings when they’re too cold can shock them even more.

Grow lights are too strong

Another reason for purple tomato seedlings (and sometimes pepper seedlings) is exposing them to grow lights that are too intense. You might experience this, particularly with new LED white lights.

Studies show that when exposed to intense white or blue lights, many plants, tomato seedlings included, produce more anthocyanins in an effort to protect themselves. This renders their leaves or stems purple and shows that they are under stress.

I own a few Mars Hydro lights (the TSL 2000W model, if you’re interested) and I’m quite happy with them. They are very strong, but fortunately, they are dimmable. The producer of these lights recommends that I start the seedlings at a 25% intensity, and increase the intensity to 100% only for the flowering stage (which I don’t need anyway).

Tomato seedlings grow like crazy under these strong LED lights – think 2 weeks instead of 4 – so if you plan on using intense lights, start them at least 1 week later than you’d anticipated.

Also, make sure that you keep your seedlings at an appropriate distance from the LED lights (unlike old school fluorescent lights that need to be as close to the plants as possible). While turning purple may be a reaction to lights, brownish-purple top leaves that touch the LED lights are a sign that your seedlings are “sunburnt” and you should move them further away from the lights.

When exposed to intense light, your tomato plant tries to protect itself. It does so by producing anthocyanins that turn the leaves purple.

Can purple tomato seedlings recover?

Purple tomato seedlings shouldn’t be a cause for concern. With indoor-grown seedlings, it’s more common than you think. Most of my tomato seedlings turn purple at some point, whether it’s the stem or a couple of leaves – or just a couple of seedlings.

I haven’t seen a difference between a purple seedling and a green one, and I’d rather have a tomato seedling that’s purple but short and sturdy, compared to a leggy one that’s a lighter shade of green.

Keep in mind that tomato plants have a long lifespan. By the time you transplant them into the ground, most signs of purple will be gone. You’ll also be doing a lot of pruning, the plant will keep growing and the stems and leaves will be exposed to natural sunlight and turn a normal shade of green.

In short, keep an eye on your tomato seedlings, don’t overwater, don’t expose them to cold temperatures, feed occasionally (but don’t overfeed), and try not to start them too early. You’ll have strong, healthy seedlings in no time.

Check out these must-have gardening products

You don’t need much to start gardening, but some tools and products will make a difference in how comfortable and effective gardening can be for you. Here are my favorites:

  • Garden Trowel. A good garden trowel will last you many years. I love how sturdy this hand trowel from WOLF-Garten is, the metal doesn’t bend and it has a nice grip.
  • Trimming Scissors. I use them for delicate pruning and harvesting all summer long, and they’re super handy. These Teflon Trimming Scissors are extra nice because they don’t rust as easily.
  • Dutch Hoe. Dutch hoes may seem old-fashioned, but there’s nothing like a quick sweep through the topsoil to get rid of small weeds – no bending required. I love WOLF-Garten’s selection: this dutch hoe coupled with their universal handle.
  • Grow Lights. These grow lights from Mars Hydro are super strong, yet dimmable, so they fit every stage of growth. They don’t put out too much heat and are very economical.
  • Seedling Trays. There’s an art to choosing the best size for seedling trays so that it holds the perfect amount of water and gives the roots enough room to grow. These germination plugs are perfect when coupled with 1020 bottom trays
  • Liquid Fertilizer. You’ll need to feed your plants from the seedling stage, all the way to fruiting. This organic fish & seaweed blend is a very versatile option. Use it half-strength for young plants and full-strength for established plants.

Browse our list of tools, fertilizers & pesticides, indoor growing products and seed shop recommendations – we hope you find our selection useful and it saves you some time!

Adriana Sim

Hi, I'm Adriana Sim, owner of Tiny Garden Habit. I practice my green thumb in beautiful Transylvania, Romania, zone 6b. While my garden is not quite tiny, it's definitely compact and super-productive. You can grow a lot of food in a small space, and it's my mission to teach you how!

Recent Posts