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Black Seeds in Tomato: Is it Safe to Eat and What Causes It?

Black Seeds in Tomato Is it Safe to Eat and What Causes It

Surprised to have found black seeds in your seemingly normal, freshly picked tomatoes? You may be wondering what has caused this and if the fruit is still safe to eat.

To set the record straight, read on as we’ve provided comprehensive answers to these questions in this article. We’ve also responded to a couple of FAQs, to boot.

Why are the seeds inside my tomato black?

Why are the seeds inside my tomato black
Image: Eat or Toss

The most common cause for black seeds in your tomato fruits is because they’re overripe. 

As they age, they get less abscisic acid, which is a hormone essential for preventing germination. Without it, the seeds begin to discolor and turn black, indicating that they’re ready to germinate.

What causes black seeds in tomatoes?

Black seeds in your tomatoes is often caused by:

  • Overripe or unripened fruit
  • Blossom End Rot (BER)

If it’s not either, it can be caused by poor growing conditions and insufficient nutrients, minerals or water.

If you’re scratching your head trying to figure out which cause best applies to your situation, read on as we explain how each contributes to the discoloration of your tomato’s seeds.

1. Over-ripened tomatoes

Over-ripened tomatoes
Image: Bon Appetit

Tomatoes have a lot of abscisic acid inside of them. This is a hormone that’s meant to help prevent its seeds from germinating.

However, as the tomato ages, the level of abscisic acid begins to decline over time. This, along with the elevated moisture levels within a tomato, can launch the germination process.

As a result, overripe tomatoes have the tendency to grow black seeds because of a process called vivipary. This is when a seed germinates even before it’s even detached from the parent plant.

In other words, it’s when conditions are right enough for the seed to begin sprouting even though it’s still inside the fruit. Thus, dark discoloration can occur, causing the seed to look black or brown. 

Since this is a sign of aging, the number of discolored seeds can vary depending on how overripe it is.

In the same vein, the darker the discoloration, the more prepared the seed is to germinate. In fact, this can sometimes happen inside the tomato.

Planter’s Tip: 

The ideal harvest time for tomatoes is when they’re at their ‘breaker stage’. This is when they’re slightly green but mostly orange-pink in color.

When you squeeze them lightly, they’re supposed to be firm and tender, yet soft with a glossy skin. 

2. Tomatoes picked too soon

Tomatoes picked too soon
Image: Garden City Harvest

On the opposite side of the spectrum, black seeds can also develop in tomatoes that were picked too soon. 

As mentioned earlier, tomatoes contain high levels of abscisic acid inside them. This helps prevent germination from happening at an unsuitable time. 

However, when a tomato is separated from its plant, it’s cut off from this essential hormone needed to grow properly. Thus, tomato seeds will begin to darken, eventually turning black. 

Hence, don’t get too excited about picking the fruits from your plant or you might be in for a surprise!

Planter’s Tip: 

If you’ve harvested your tomatoes prematurely, you can fix this by trapping the ethane gas which can quicken the ripening process by:

Storing the tomato in a paper bag and keeping it at a warm location
Keeping a ripening banana beside the premature tomato

3. Blossom End Rot (BER)

Blossom End Rot (BER)
Image: USU

Seasoned tomato growers are often familiar with Blossom End Rot, or often simply referred to as BER. 

While tomatoes with BER look like they came out straight from a horror movie, the good news is that it’s a non-infectious, physiological disease. 

It primarily affects the bottom portion of the tomato, also called the blossom end, which begins to gradually break down and rot. 

While BER is typically observed outside of the fruit, it can also cause black seeds along with internal browning or blackening inside the tomato. 

BER can be caused by several sources, such as:

  • Localized calcium deficiency
  • Excessive or uneven watering
  • Drought
  • Freezing

Contrary to popular belief, BER isn’t caused by fungi. If you’ll notice, the causes listed above are all environmental factors.

While tomatoes affected by BER can’t be salvaged, gardeners can narrow down the factors to whichever applies to their circumstances. This way, you can prevent the recurrence of BER in your succeeding yields.

How to Fix It

If you’re adamant about saving your tomato plant and its future fruits, here are a couple of ways that you can be your plant’s hero and fix BER:

1. Boost calcium content

As mentioned earlier, BER is typically caused by a localized calcium deficiency. Having said that, the first thing you’ll want to do is raise calcium levels.

You can add any of the following calcium-rich materials onto the base of your tomato plant or mix it into the soil for optimal absorption:

• Crushed eggshells
• Coffee grounds
• Gypsum
• Powdered lime
• Wood ashes
• Calcium-based foliar spray
• Calcium nitrate powder

2. Regularize your watering routine

BER can also be caused by an irregular frequency and quantity of your watering. To combat this, you’ll want to set a specific time of the day to water your plant and a fixed amount.

It’s often highly suggested to water your plants first thing in the morning. This is because the sun isn’t hot enough to evaporate the water yet, giving your plant enough time to thoroughly absorb it.

In a week, tomato plants need about 1 to 2 inches of water. Since they’re typically grown in containers, they need a bit more water than in-ground-grown tomatoes.

In the height of summer, you may need to increase the amount of water you’re giving your plant.

More often than not, a common practice is to simply water your tomato pot until it begins to drain from the bottom. Afterward, let the soil dry up a bit before your next watering session.

4. Other unknown causes

Other unknown causes
Image: Houzz

Although it doesn’t make sense that there are discolored seeds in a seemingly fine tomato fruit, it sometimes just happens. 

While it may seem that they’ve been caused by a variety of unexplainable factors, they could also simply be a natural cause. 

There’s also a possibility that the tomato wasn’t able to develop properly due to:

  • Exposure to extreme temperatures
  • Lack of water
  • Lack of fertilization
  • Lack of nutrients and minerals
  • pH imbalance

Even then, it may also simply be an odd case if only one tomato has developed black seeds while the rest of the yield is perfectly fine.

Is it safe to eat the black seeds inside tomatoes?

Is it safe to eat the black seeds inside tomatoes
Image: Taste of Home

If the tomato doesn’t show any indication of a disease, then it’s perfectly fine to consume even with black seeds. More often than not, it’s usually just overripe.

While having tomatoes with black seeds isn’t normal, they aren’t known to cause any harm when eaten as the discoloration is typically just a sign of aging.

Nevertheless, it still all boils down to your preferences as some may feel discouraged to eat food that doesn’t look like it normally should.

So if you feel grossed out by the black seeds in your tomato, feel free to toss it in the garbage or, better yet, compost it.


What are the black spots at the bottom of my tomato fruit?

The discolored spots, often brownish-black, at the bottom of your tomato are most likely blossom end rot (BER). This disease affects the appearance of your fruit, causing it to rot from the bottom.

Is it safe to eat tomatoes with seeds sprouting inside?

It’s perfectly fine to eat tomatoes with seeds that have already begun to sprout from the inside. This simply means that they’re overripe and ready to germinate.

Can I eat tomato seeds?

It’s safe to eat tomato seeds. In fact, they’re known to be of great help in improving one’s metabolism, digestion, and gut health. 

However, most cooks don’t add tomato seeds to their dishes because of how watery they are. This can cause the flavor of the food to be watered-down.

How can I tell if a tomato has gone bad?

If a tomato is wrinkly, mushy, smelly, and leaks any fluid, then it’s gone bad. On the bright side, they’re still safe to eat.

Good tomatoes are supposed to be relatively blemish-free with bright, soft, and tight skin.

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