Blossom End Rot: Why Your Tomatoes Have Black Bottoms

Do your tomatoes have black bottoms this season? This is quite common, and is typical of blossom end rot. In this article, gardening expert and former organic farmer Logan Hailey walks through everything you need to know about blossom end rot, including how to treat it, and how to prevent it.


It’s mid-summer and you’re finally ready to harvest those delicious tomatoes you’ve been tending all spring. But just when you’re craving the perfect Caprese salad or fresh pico de gallo, you notice a weird black rotten spot on the butts of your tomato fruits.

Blossom end rot is a common problem for tomato gardeners around the world. Although it looks like a gnarly tomato disease, it’s actually a cultural issue that has to do with the soil minerals and moisture levels. While you can’t fix fruit that has already begun to rot, you can take steps to mitigate future problems.

Let’s dig into everything you need to know about blossom end rot and how to prevent this problem in your tomatoes!

What is Blossom End Rot?

Tomato with Black Bottom
This issue affects the bottoms of tomato fruits due to excess nitrogen in the soil, improper watering and low soil pH.

Blossom end rot is a physiological disorder of tomatoes most commonly caused by a calcium deficiency in the soil. Inconsistent watering, a low soil pH, and excessive nitrogen can also cause the issue.

This nutritional problem leads to black, gray, or brown areas that appear sunken-in or water-soaked. These rotten regions occur on the bottom end where the tomato flower once was (hence the name).

Blossom end rot can also affect zucchini, squash, peppers, eggplants, and watermelons. It most commonly appears in the early summer when the first fruits begin to develop. While it may seem alarming, it is typically easy to fix and resolves itself in the next round of fruiting.

Key Symptoms

Tomatoes with Brown Dying Bottoms
The main symptoms you’ll notice are black or brown leathery tissue and fruit rot.

Blossom end rot is one of the most easily recognized tomato problems. Symptoms rarely show up in cherry tomatoes, however they can be very obvious in large plum, paste, and slicer-type tomatoes.

Symptoms include:

  • Water-soaked lesions on the bottom of ripe tomato fruit.
  • Mushy or mall-formed spots on the blossom-end.
  • Bruises on green fruit.
  • Black or brown leathery tissue.
  • Dark, rotten tomato “butts” (due to secondary fungal and bacteria diseases).
  • Premature fruit decay.


Yellow and green tomatoes with black bottoms
The main causes of tomato rot damage are lack of calcium, low soil pH, and insufficient or excessive watering.

While a lack of calcium is the most obvious cause of blossom end rot, a surprising number of factors can affect the calcium levels in your soil. Soil minerals are intricately intertwined and an excess of one can often affect the plant availability of another.

Similarly, soil pH and moisture levels impact how “available” a mineral is to plants. In other words, some plant nutrients (like calcium) cannot be used by a plant under certain conditions.

The primary and secondary causes may include:

Calcium Deficiency

Calcium is a plant nutrient required in a large quantity while tomatoes are rapidly developing fruits. You can think of calcium (Ca) as the “glue” to cells. It holds the fruit cells together to make tomatoes firm. It is a vital plant nutrient for producing strong cell membranes and cell walls.

As cells quickly grow and replicate during the tomato fruiting phase, insufficient calcium leads to poor development of tomato cell walls and skin. This manifests as mushy or deformed spots on the bottom of the tomato. Secondary infections lead to rapid ripening, rotting, and premature decay of the fruit.

Low soil pH

Even if there is enough calcium in the soil, the roots of your tomato plants may not be able to take it up. Acidic soils with a pH below 6.0 tend to have very low calcium availability.

The optimal soil pH range for calcium availability is between 6.5 and 8.5. A basic soil test can help determine if your soil needs amending.

High Nitrogen Fertilizer

While pumping your soil full of nitrogen-rich fertilizer seems like a good idea for heavy-feeding tomato plants, an excess of nitrogen can actually do more harm than good. High nitrogen levels inhibit the availability of calcium in the soil.

Cold Soil

Tomatoes are warm-weather crops that cannot uptake nutrients very well in cold soils. You may notice it occurring more often during cool spring or fall weather. Using landscape fabric, plastic mulch, or a greenhouse can help keep the soil warmer for better calcium absorption.

Water Stress

Tomatoes are not very picky crops, but there is one thing they really prefer: consistent moisture! Alternating long periods of drought with sudden flushes of water can cause the plant to be stressed, often exacerbating calcium imbalances and leading to this common problem. These fluctuations in water are also linked to tomato splitting and cracking issues.

Similarly, frequent shallow-watering can lead to shallow root development and poor calcium uptake. On the other hand, waterlogged soils or heavy soils with a compaction layer also pose a problem. Needless to say, tomatoes don’t want things too dry nor too wet. Balanced and consistent irrigation are the key to prevention!

If this seems like an over-exaggeration, consider that susceptible plants (such as those already growing in calcium-deficient soils) under water stress for as little as 30 minutes can get blossom end rot.

Don’t worry, this doesn’t mean you have to put a baby monitor in your tomato bed! Instead, use our proven strategies below to modulate soil moisture.


Once a tomato fruit gets blossom end rot, you can’t do anything to reverse it. However, you can quickly take action to prevent the issue as the plant continues producing. Just because a plan produced a few tomatoes that end up with black bottoms, does not mean that all its fruit will be inedible. These methods can be used right away or in preparation for next season.

Apply a Foliar Calcium Spray (Quick Fix)

spraying tomatoes with Foliar Calcium spray
It is recommended to use a foliar calcium spray to increase calcium levels.

A foliar spray is the quickest way to boost calcium levels and save your upcoming tomatoes from this quick developing problem. This means you dilute a readily available calcium fertilizer (per package recommendations) and spray it directly on your tomato leaves so they can quickly absorb it through their leaf stomata.

You can purchase a premade option or make a DIY version. Our top foliar calcium spray recommendations include:

You can also make a DIY Calcium Spray yourself. You’ll need to gather at least 10 clean egg shells, dry them out, crush them, and put in a mason jar field with vinegar. Wait until the solution stops bubbling and completely settles, allowing it to infuse for at least a few days. Dilute to 4 tbsp. per gallon of water and apply.

Be sure to use foliar sprays in the evening when it has cooled down. Otherwise, you may inadvertently burn the leaves of the plant in the harsh sun.

Remember that a foliar spray will only provide a quick dose of calcium and won’t fix the underlying cause of the problem.

Improve Soil Calcium Levels (Long-Term)

High quality garden soil
To increase the level of calcium in the soil, calcium supplements can be applied.

Building soil calcium levels requires a more holistic approach than simply applying a quick fix spray. Although calcium is very immobile (slow-moving) in the tomato plant itself, it is considered highly mobile in the soil.

This means it can easily be lost to leaching. In areas with heavy rainfall or excessive irrigation, calcium levels are often lacking because the mineral has been washed away with soil particles. Depending on your soil tests, you may need to amend with calcium every season.

Some gardeners prefer to add a source of organic calcium at the time of planting tomatoes in the garden. Crushed eggshells or oyster shell fertilizer can easily be tossed by the handful directly in the planting holes.

These amendments work best when mixed into the soil 6-7” deep, but they can also be mixed into the surface layers after tomato plants are already growing.

Maintain Consistent Soil Moisture

watering tomatoes
When it comes to prevention, it’s necessary to balance your watering schedule.

Uneven watering has a direct impact on plant uptake of calcium. Finding a balance with soil moisture is the most important cultural method for prevention. The soil in your tomato beds should never totally dry out, nor get soggy and waterlogged.

You can make soil moisture more consistent by:

  • Checking soil moisture every other day.
  • Deeply water tomatoes a few times per week to improve water penetration.
  • Utilizing straw, grass clippings, or leaf mold as mulch around the base of tomatoes.
  • Irrigating with drip lines or soaker hoses on timers.
  • Ensuring high levels of organic matter.

Whatever you do, try to avoid massive fluctuations in the watering frequency of your tomatoes. Don’t allow the soil to become bone dry in between rains or watering.

Adjust Soil pH

pH measure meter
Make sure the soil pH is between 6.5 and 8.5.

Acidic soils are particularly prone to low calcium levels. A soil pH 6.5 and 8.5 is optimal for calcium absorption. After performing a soil test, determine if you need to raise your pH or if it’s already in the optimum range.

Heavy clay soils tend to be more acidic and may require an alkalizing agent to make calcium more available.

Raise pH levels with:

Avoid Excess Nitrogen Fertilizer

chemical fertilizer for tomatoes
If it does appear, do not apply fertilizers with a high nitrogen content to tomato beds.

If you are dealing with blossom end rot in your garden, don’t amend tomato beds with fertilizers that are high in nitrogen. Too much nitrogen can actually hinder the calcium absorption of plants because it makes plants grow so fast that they cannot accumulate enough calcium to keep up.

This is particularly problematic when using a quick-release synthetic fertilizers. Instead, opt for balanced nitrogen fertilizers and/or slow-release organic fertility.

Avoid These Nitrogen FertilizersChoose These Balanced Fertilizers
Ammonium nitrateAll-Purpose Organic Granular Fertilizer
AmmoniaComposted Manure
UreaFeather Meal or Blood Meal

Improve Soil Organic Matter

Handful of composted soil in hand
To improve the quality of your soil, add compost or mulch from rotted leaves.

Organic matter or humus simultaneously improves the drainage and water holding capacity of your soil. This is important for preventing tomato diseases while maintaining consistent moisture and preventing calcium leaching.

Use one or more of these materials to improve soil organic matter levels:

  • High quality compost.
  • Rotted leaf mulch.
  • Fully aged manure.
  • Cover crops or “green manure” like peas and oats.

Wait for the Next Fruit Flush

delicious green and red ripe tomatoes
If you do not have the above problems, then wait for the next harvest of tomato fruits.

Sometimes it only becomes an issue in the first round of tomato fruiting. This is why it so commonly alarms gardeners in the spring. If you don’t think you are facing any of the issues above, you may simply need to wait a couple of weeks for the next flush of tomato fruits.

Final Thoughts

Mushy black bottoms on your tomatoes may look unsightly and frightening, but they aren’t the end of this season’s tomato crop. Because blossom end rot is a physiological issue rather than a disease, it can easily be solved from the ground-up.

Quick sources of calcium such as baking soda, wood ashes, or foliar sprays can rapidly improve blossom end rot issues. Then, you can focus on evening out your watering regimen while improving soil mineral balance and pH.

A bountiful tomato garden overflows with plump, vibrant fruits, some tinged with vivid red while others hold onto their youthful green. A plastic watering can hovers above the tomato vines, releasing a gentle, life-giving cascade of water droplets.


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