Dealing with Tomato Diseases

GROW — practical gardening tips

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Tomatoes, alas, are not the easiest vegetable to grow. Here in the Midwest and most of the U.S.A. our growing season is not long enough, so we have to buy seedlings and transplant them into our gardens. In addition, weather conditions and pests cause other problems. Just look at the “common issues” that the Bonnie Plants website lists with many of its tomato plants, even with its “super disease resistant” varieties:

Common issues: Plants may stop setting fruit when temperatures dip below 55˚ F or climb above 90˚ F. Blossom end rot can be a problem, as can misshapen fruit.

bonnieplants.com

I remember fondly my early years of gardening when those common issues like blossom end rot and low fruit set were all that I had to worry about . If you are still in that situation, count your blessings and garden on! But don’t be naive about it—do everything you can to prevent fungal and bacterial diseases from starting in your garden. Once they come, they overwinter in the soil and keep coming back. Since our summers tend to be rather humid, such diseases flourish here. I’ve had some form of tomato blight every year since the first time I saw spotted and yellowing leaves on my plants.

Here is a rundown of what I do to prevent soil-borne diseases on my tomato plants and to keep them from spreading once they make their inevitable appearance.

1. Water from below—never spray water onto the foliage. This, by the way, is a good rule to follow for all plants if you live in a climate with high humidity. Many other plants are also susceptible to fungal diseases that are spread by overhead watering. You always want to water the plants’ roots, not the leaves. I use soaker hoses in my raised beds. Whenever I use the regular hose for watering, I attach a long water wand to it so that I could direct the water down toward the roots without bending over.
2. Mulch to prevent rain from splashing soil up onto the plants. Years ago I used sheets of red plastic in my beds. Then I got Tomato Craters, the round red plastic things around the bottoms of my tomato plants which everyone always asks me about. These hold up better from year to year and give me more flexibility in placement of the plants. There are similar products available now which may work better at directing water down to the root zone, called Tomato Automators and Tomato Halos or Plant Halos. For my container tomatoes, I put wood mulch around the plants. (Here’s a video about how I set up the Tomato Craters, soaker hoses, and support cages when I plant tomatoes.)
3. Space plants farther apart to improve air circulation. I do space my tomatoes further apart than I used to, but I never got to the minimum ideal of at least 4 ft. apart in all directions. I get fairly close to that in my 4’x10′ raised beds by planting four tomatoes on each side for a total of eight in each bed. I used to plant three more tomatoes down the middle, but in 2020 I switched to planting a row of bush beans down the middle of my tomato beds instead. The bush beans are good companion plants for tomatoes. I also put two celery plants between the tomatoes. Intercropping like this makes good use of the room created by spacing the tomatoes farther apart, and it also cuts down on weeds in the bed. And because I can’t stand the thought of growing fewer tomatoes, I began growing even more tomatoes in containers. (Here’s a video about these changes in my garden.)
4. Rotate crops. Moving vegetables that are in the same plant family to different locations in the garden keeps the pests and pathogens attracted to those plants from building up in the soil year after year. Crop rotation also has other benefits, such as avoiding the depletion of each plant family’s favorite nutrients. I have six raised beds for rotating my vegetable plants, and I usually fill two of them with tomatoes and a couple tomatillos. I use containers for growing more tomatoes and all other vegetables in the nightshade family (Solanaceae): peppers, eggplants, potatoes, and ground cherries. By alternating the two tomato beds among my six raised beds, I achieve the recommended minimum of three years of rotation. Five to seven years would be more effective, but I’m not ready to cut back to just one bed of tomatoes.
5. Prune plants well, early, and frequently. Removing suckers improves air circulation. Removing the lower branches prevents fungal spores from splashing up from the soil onto the leaves. I tend to get diseases, such as early blight, that work their way from the bottom of the plant up. I used to put this task off until I saw a fungal disease already beginning to affect the lowest leaves. I have since learned to start trimming those lower branches right away. It is also important to look for and remove diseased leaves throughout the plants as soon possible.
6. Disinfect pruning tools between plants to prevent the spread of disease. When pruning my tomato plants, I spray or wipe my clippers with rubbing alcohol before moving on to the next plant. I do not recommend using bleach because it is corrosive and it requires at least a ten-minute soak to be effective. I have actually gone back and forth, as noted in my earlier post, between using alcohol and using Lysol to disinfect my pruners. More recent Extension Service articles indicate that either ethanol or isopropyl alcohol is more effective against most plant pathogens. Whatever product you use, I also recommend wearing disposable gloves while pruning tomato plants. Both the tomato plants oils and the sprays can be irritating to bare skin.
7. Spray the plants with an organic fungicide. This strategy also works best when you do it early and frequently. There are several kinds of organic fungicides, and it may take you some trial and error to find the one that works best for the disease issues in your own garden. Years ago I used a copper fungicide called Soap-Shield, but later I had better success with a biofungicide called Serenade, which had Bacillus subtilis in it. However, the home garden sized version of this product was discontinued. Now there are several biofungicides available with different strains of the related bacteria, Bacillus amyloliquefaciens, including Arber (strain F727), Bonide Revitalize, and Monterey Complete Disease Control (both of these last two have strain D747). In 2026 a new biofungicide, Magic Gardener, has come out with what its manufacturer says is a higher potency strain of Bacillus amyloliquefaciens, PTA-48. The manufacturer sent me samples to try and to share with others* (see note in comments) in 2025, but our weather that summer made for a difficult test case. Since it fluctuated between periods of no rain and then heavy rains, I could not tell if Magic Gardener really helped or not. I will use it again this year and share an update later. I do have high hopes that it will work even better than Serenade did.
8. Clean up! Clean up! Clean up! Remove the plants and as much of their debris as possible at the end of the season. We top the raised beds composted manure every fall. Clean and disinfect the cages and other staking tools. I’ve always been careful to wash the Tomato Craters, and I usually leave the cages outdoors in sunlight and rain to sanitize them. Sometimes I spray or wipe them down with Lysol, too.

Those are my recommendations for dealing with fungus and bacterial diseases in tomatoes. If you find yourself dealing with fungus and bacterial soil borne diseases every year, there is one more option that you may want to try. When planting tomatoes next year, you could apply a root protection drench, such as Bioworks Rootshield or Gardens Alive Root Guardian. I had great success with the latter the first time I tried it, and Gardens Alive put my glowing review in their catalog and on their website. Unfortunately, the next year they sold me some that was too close to its expiration date and it was ineffective. It has a very short shelf life and is rather expensive. I then switched to the Bioworks product, but the next year’s rainy spring made it a bad year for my tomatoes even though I’d done my best to get fresh product and apply it properly. I have not tried it since.

This post, a follow-up to an earlier post, Fight the Blight, was updated in 2022 and then again in 2026. If you found it helpful, please share it! You may also leave a reply below to let me know how your tomatoes are doing. Stay tuned for future developments in my ongoing fight against tomato diseases.