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Help! My Tomato Seedlings are Purple! (Fix Them Quickly & Easily)

Woman's hand holding a purple tomato seedling between her fingers
Purple tomato seedlings can be a shocking discovery. Luckily, it’s an easy problem to fix.
Photo credit: Tracey Besemer

Tomato plants are green. In fact, I’d go so far as to say most of your vegetable seedlings are green.

Thanks, Tracey. I appreciate you pointing out the obvious. What’s your point?

My point is this: knowing tomato plants should be green means it comes as a bit of a shock when you wake up one morning to find that your tomato seedlings are purple.

To be fair, this change usually takes a week or two, but it always seems to be the case that we don’t catch it until we’re staring at purple tomato plants, wondering what happened.

Now, before the panic sets in, your seedlings will be fine.

Believe it or not, this is a common issue that pops up with tomato seedlings. The issues at play are easy to diagnose and even easier to fix. With a few changes, your plants will be a healthy, recognizable green by next week.

Why Purple?

Fingers holding a small tomato seedling that has turned purple
It looks much worse than it is. Purple tomato seedlings are easy to fix.
Photo credit: Tracey Besemer

I’m assuming you’re here after making this shocking discovery for yourself. You’ve checked your seedlings and noticed:

  • purple stems
  • the undersides of the leaves are purple
  • the veins on the leaves are purple
  • in advanced cases, even the tops of the leaves can begin to turn purple

It all boils down to a lack of nutrients, specifically phosphorous. When plants don’t receive enough phosphorous, they will cope by creating more anthocyanins (the flavonoid responsible for, you guessed it, making purple plants).

Fingers holding a tomato leaf that has purple veins from a phosphorous deficiency.
The veins of this tomato seedling have turned deep purple.
Photo credit: Tracey Besemer

Thankfully, this tell-tale sign lets you know right away that your tomatoes need more phosphorous.

A Few Causes for Nutrient-Deficient Tomato Seedlings

There are a number of reasons why seedlings may be deficient in specific nutrients. Figuring out which one applies to your situation will also provide you with the appropriate fix to remedy the situation quickly.

No Fertilizer

Fingers holding a tomato seedling stem that is recovering from phosphorous deficiency
This was a week after I added fertilizer. You can see that the stem is already greening up again.
Photo credit: Tracey Besemer

This is the most obvious reason why your seedlings might be lacking. The cotyledon provides new plants with all the nutrients they need to develop from a seed to a seedling. However, once secondary leaves show up, you will need to begin feeding seedlings with a balanced fertilizer to ensure large, healthy plants.

The fix here is simple: feed your green babies. An organic liquid fertilizer with a balanced NPK ratio is the best option for new plants. Start feeding at half-strength.

“But Tracey, I have been fertilizing my seedlings.”

If that’s the case, then it’s more likely the seedlings are unable to use the nutrients you have provided.

The Roots Are Unable to Take Up Nutrients

Fingers supporting a small tomato seedling that has turned purple due to a nutrient deficiency.
There are a couple of reasons why seedlings might not be able to take up nutrients. Both are easy to diagnose and fix.
Photo credit: Tracey Besemer

The soil is too cold.

When soil temps fall below 50 degrees, it can slow or even stop the roots of tender tomato plants from being able to absorb nutrients properly. Remember, these are warm-weather plants.

Like many gardeners, I start my seedlings indoors late in the winter, which means my home is still quite cool at night. To keep my plants happy during this critical growth period, I use heated seedling mats under my seedlings. They’re great for germinating seeds and keeping the soil at a consistent temperature, even at night when my house is cool. (Here are the ones I use. They’re great.)

Your plants need to be potted up.

If you start seedlings in tiny seed-starting cells, they need to be potted up pretty quickly. If you let them go for too long, they will become root-bound and essentially stop growing. The seedlings will no longer be able to take up nutrients efficiently due to the inadequate root system.

Purple-stemmed tomato seedling
Cramped in a tiny seed-starting cell, this tomato plant was unable to form roots that would allow it to take up nutrients properly.
Photo credit: Tracey Besemer

Again, this is an easy fix: simply pot up your seedlings. This will allow them room to form a larger root system.

When In Doubt, Fix All the Issues

Woman's hand holding potted up tomato plant.
Fix all the issues in one go!
Photo credit: Tracey Besemer

I’ve found the easiest fix is to tackle all of these issues at once. Rather than trying to figure out which scenario could be causing a phosphorous deficiency, it’s easier to eliminate all possible causes.

Repot seedlings into a larger pot and water them well. Include a balanced liquid organic fertilizer at half strength. Then move them to a location that doesn’t fall below 60 degrees at night, or use a seedling heating mat to keep them warm.  

What a difference a few days can make! The leaves on this seedling are recovering from the bottom up.
Photo credit: Tracey Besemer

You probably noticed that the issues that cause purple tomato seedlings stem from something preventing the plant from being able to take up nutrients. By fixing the phosphorous issue, chances are, you’ll be fixing more than one deficiency.

It’s quite common in these scenarios for your plants to be deficient in all key nutrients; it just so happens that a lack of phosphorous gives us the most obvious clue.

Fingers holding the stem of a purple tomato seedling
A week later, the purple color has lessened, and the seedlings are looking much greener.
Photo credit: Tracey Besemer

Within a week or so, you’ll be well on your way to healthy, green seedlings once again.

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Tracey Besemer

Hey there, my name is Tracey. I’m the editor-in-chief here at Rural Sprout.

Many of our readers already know me from our popular Sunday newsletters. (You are signed up for our newsletters, right?) Each Sunday, I send a friendly missive from my neck of the woods in Pennsylvania. It’s a bit like sitting on the front porch with a friend, discussing our gardens over a cup of tea.

Originally from upstate NY, I’m now an honorary Pennsylvanian, having lived here for the past 18 years.

I grew up spending weekends on my dad’s off-the-grid homestead, where I spent much of my childhood roaming the woods and getting my hands dirty.

I learned how to do things most little kids haven’t done in over a century.

Whether it was pressing apples in the fall for homemade cider, trudging through the early spring snows of upstate NY to tap trees for maple syrup, or canning everything that grew in the garden in the summer - there were always new adventures with each season.

As an adult, I continue to draw on the skills I learned as a kid. I love my Wi-Fi and knowing pizza is only a phone call away. And I’m okay with never revisiting the adventure that is using an outhouse in the middle of January.

These days, I tend to be almost a homesteader.

I take an eclectic approach to homesteading, utilizing modern convenience where I want and choosing the rustic ways of my childhood as they suit me.

I’m a firm believer in self-sufficiency, no matter where you live, and the power and pride that comes from doing something for yourself.

I’ve always had a garden, even when the only space available was the roof of my apartment building. I’ve been knitting since age seven, and I spin and dye my own wool as well. If you can ferment it, it’s probably in my pantry or on my kitchen counter. And I can’t go more than a few days without a trip into the woods looking for mushrooms, edible plants, or the sound of the wind in the trees.

You can follow my personal (crazy) homesteading adventures on Almost a Homesteader and Instagram as @aahomesteader.

Peace, love, and dirt under your nails,