BONNIE’S GARDEN – What Can Go Wrong With the Fruit on Your Tomatoes and How to Fix It

I’ve had so many customers come in recently with tomatoes in their hands because they have a problem with the fruit. If you’re growing tomatoes, here is a list of what you may find, the cause, and how to mitigate the problem.

Blossom End Rot

Blossom end rot is water-soaked lesions at the bottom of the fruit. This is caused by a calcium deficiency—but it may or may not be due to a lack of calcium in the soil. Other factors that can affect a plants uptake of calcium may be:

Planting too soon

If you plant when soil temperatures are below 65 or so, this can affect the plant’s ability to uptake nutrients from the soil.

Using a high nitrogen fertilizer

Use a fertilizer with more phosphorus than nitrogen. Tomato-tone by Espoma is my favorite fertilizer, but if it isn’t available, then Flower-tone or Garden-tone is good.

Inconsistencies in soil moisture

Never ever let a tomato go so dry it begins to droop, but, also never water if the soil is still dark and moist to the touch.

A soil pH that is too alkaline

Get your soil checked.  Tomatoes prefer soil with a pH of 6.0 to 7.0.


Cat facing is a disorder that causes deformity on the bottom of the tomato—scar tissue filled cracks, abnormal cavities, and small swollen bulges. The exact reason why this happens is not known, but it does seem to center around environment stresses that can cause incomplete pollination. Possible causes:

  1. Planting too soon, when soil temperatures are too cold
  2. Excessive heat and humidity
  3. Inconsistent watering


Cracks in the stem end of the tomato. This is usually caused by inconsistent watering. Heirloom tomatoes, particularly beefsteak types, seem to be more prone to both cat-facing and cracking—and yes, this does include my favorite tomato, Cherokee Purple.

Not setting fruit

One annoying thing about tomatoes is they often stop setting fruit when daytime temperatures are over the low nineties. While tomatoes are self-pollinating, in excessive heat and humidity, the pollen can degrade so it “clumps” making it difficult to self-pollinate.

Mulch around the roots with an “airy” mulch like straw to keep moisture even and keep the roots cooler. Do NOT feed during excessive heat! Plants don’t want to be forced to grow when they are under weather stress.

Fruits with holes eaten in them

This can be caused by one of two things—birds or squirrels. I’ve actually seen cardinals perched on the sides of my tomato cages pecking the heck of the ripe tomatoes—after the moisture content. Pick the tomato when it’s “mostly” ripe and let it finish on the windowsill. Also, provide a water source elsewhere.

If you’re finding green tomatoes with one bite missing, that is likely squirrels also looking for the moisture. The cure is simple—spray green tomatoes with a repellent—like Hot Pepper Wax (an extract of cayenne pepper), and provide an easily accessible water source 10 to 15 feet away—a birdbath or saucer filled with water.

It’s a matter of survival—if you don’t provide an easy water source, they’ll go after the tomato anyway.

Let Us Help You

If you’re having a weird problem with your tomatoes—or any veggie—come in and let us help.

As a matter of fact, if you are having ANY gardening problem, stop by and let us help you solve it. That’s why we’re here!

To read more posts from Bonnie, visit our blog

11 thoughts on “BONNIE’S GARDEN – What Can Go Wrong With the Fruit on Your Tomatoes and How to Fix It”

  1. I have big thick beautiful tomato plants with no blooms or tomatoes. They were not planted early either. What could cause that? Thanks

    • Several things can cause tomatoes to not bloom well—first is lack of enough sun light. Tomatoes need six hours or more of direct sun. The other thing could be too much nitrogen. If you use a lot of cow manure or poultry manure that can be a problem because animal based manures are very high in nitrogen. Nitrogen promotes beautiful bushy plants at the expense of flowers. When you feed tomatoes (and they should be fed regularly) be sure to use a fertilizer with a slightly higher middle number–that’s phosphorus. I like tomato-tone but if it’s not available, Garden-tone or Flower-tone are good. Just make sure the middle number (phosphorus) is a little higher than the first and last numbers. One last thing, depending on the variety of tomato, some are not as heat-tolerant as others. This year we had 21 days straight of heat over ninety degrees. Tomatoes are a little stressed at those temps.

  2. I also found a great video on YouTube about ways to manually pollinate your tomatoes – and it’s working so far! I learned about tomatoes being self pollinators; the pollen falls into the stamen if the flower (and hopefully fertilizes it) when it’s gently touched, much like a bee might do. Another method is to use an electric toothbrush to GENTLY vibrate the flower so that the pollen is released. I’ve been doing this with success. Just be sure to use an old toothbrush head, as it will get green and sticky.

    • Thanks so much for the tip. I usually just walk by and “shake” mine, but this would be good to know during excessively hot weather.

    • A lot depends on what Mother Nature does from here on out. Tomatoes will usually keep producing into the fall, but an early frost will kill them. Our first frost here is usually mid-end October. Start checking the long-range weather forecast early October and it looks like frost is forecast, pick all the green tomatoes and bring them in to a windowsill to ripen. In the meantime, keep your tomatoes watered when necessary and fertilized.

  3. My tomato leaves have brown spots the eventually turn the entire leaf brown. I still get tomatoes, but my vines look diseased. What is this?

    • There are a number of diseases that can attack tomato plants, some fungal, some bacterial, some viral. A couple of the most common problems this late in the season are Septoria Leaf Spot and Late Blight. Unfortunately, the solutions are not 100%. You can pick off the worst of the leaves (and get up any that may have fallen on the ground), try to keep water off the foliage when you water and treat with an organic fungicide such as Neem oil. That might buy you some time. Ideally, and I know it is hard to do–pull the diseased plants up and dispose of them (do NOT compost). And the bad news–do not plant another tomato, eggplant tomatillo, potato or pepper in that spot for THREE years as the pathogens can live that long in the soil. You can plant beans, cucumbers, squash, etc. just not tomatoes and relatives. And, if you decide to try the first suggestion, you still need to pull the plants up and dispose of them at the end of the season and not plant another tomato family member for three years.

  4. About zucchini crook neck and yellow squash I planted as plants from the Bonnie plant cups on 5/16/20 in all organic raised bed garden. Why are they making the yellow flowers which stay closed stay on stem for few days then drop off or 1 looks like snipped off (garden is fenced) but never produce not 1 squash so far. I figured I’d be up to my eyeballs with them by now. Ideas? Suggestions? I’m not a newby gardener have been gardening since pre kindergarten age now Im old as dirt (68). Had gardens from New England to here

  5. Cynthia–Especially hot and humid weather can affect the development of pollen–the premature death of pollen grains or especially show growth of pollen tubes. That can make flowers fail to open. Flowers are only open for a very short period time anyway. If the female flowers (ones with the tiny fruit at the base) are falling off, that is from lack of pollination.

  6. Dot, I’m afraid you DO have a disease–tomatoes are prone to both viral, bacterial and fungal diseases–though this summer with excessively hot and humid weather, I’m banking on fungal. Next year, do NOT plant another tomato, pepper or eggplant (they’re related) in that same spot. Plant cukes or squash or beans, but move tomato family members to another area as these diseases can linger for two three years in the soil.

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