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The Garden Scoop

Tomato Problems and Solutions

A ripe tomato on a tomato plant.

Tomatoes are one of the most planted garden crops in the US and remain a staple of most vegetable gardens across central Illinois. Illinois Extension receives many questions about these plants and their care each year, with most questions centering on controlling some common ailments.  From dead portions of the plant to insects eating leaves or even damaged fruit at harvest time, there are quite a few common ailments of this garden staple.  Many gardeners seek a complex set of solutions and processes to solve these issues. However, relatively easy cultural practices can take care of most common tomato problems.




A tomato hornworm
Tomato hornworm on a tomato plant. Photo: Ryan Pankau
Tomato Hornworm

Perhaps the foremost insect pest on tomato plants, the tomato hornworm (Manduca quinquemaculata), is about to appear for the 2023 growing season. These defoliating larvae emerge from pupa in July after overwintering in the soil. They are native to North America with a large home range spanning sea to sea.

Identifying the damage that ensues after they hatch is often very easy. The little critters are big consumers of leaves, fruits, and smaller stems on tomato plants, leaving very noticeable damage in as little as a day. I have always had excellent control from timely hand removal of these caterpillars, but it does take a watchful eye.

During the daytime, these guys hang out in the shady lower portion of the plant, waiting for their favorite time to feed after dark. At night, they are easily found feeding in the tiptops of plants. I make the rounds each evening to quickly pluck them off the branch tips as they are fully displayed in the moonlight. Daytime control efforts often take quite a bit of additional searching, and it's hard to find them all.

Concentric circles of early blight on tomato leaf
Concentric circles of early blight on tomato leaf. Photo: Ryan Pankau
Early Blight

Early blight is a foliar disease caused by the fungal pathogen Alternaria solani. It appears as yellow spots on lower leaves which enlarge into concentric dark brown spots, eventually withering and killing infected leaves. The disease always originates on lower, older leaves and moves upward, creating a noticeable pattern. As the infection worsens, it attacks petioles, stems, and fruits. A. solani overwinters in infected plant debris at or near the soil surface. During favorable spring conditions, the fungi produce spores that are spread by splashing raindrops or wind to infect leaves. 

Since this pathogen moves from soil to leaves, a mulch barrier is one of the most effective control measures. I’ve had excellent control of this condition by mulching immediately after planting my tomatoes, offering no opportunity for raindrops to splash the fungi onto leaves. Watering plants with drip irrigation or a soaker hose can also help immensely. Providing good air circulation by staking plants and pruning excess foliage can limit its spread by reducing favorable conditions, such as wet leaves.

septoria leaf spot
Symptoms of septoria leaf spot. Photo credit: University of Illinois Extension Plant Clinic
Septoria Leafspot

Septoria leafspot is another fungal pathogen that infects leaf tissues.  It is characterized by small black spots on leaves, with centers that later turn white and develop tiny black dots.  This disease also begins on lower leaves, thriving in wet weather and spreading up the plant. It is transmitted from the soil, much like early blight, with control recommendations identical for each pathogen. 

Both of these fungal diseases can also be addressed by keeping plants healthy to limit susceptibility.  Good fertilization (but not over-fertilization) is part of that strategy including a starter fertilizer at the time of planting, a side-dress application when fruits are about golf ball sized, followed by 2 more applications (spaced out 3-6 weeks) throughout the growing season.  Follow product instructions for the recommended rate for each application.

blossom end rot on tomatoes
This tomato is showing the early signs of blossom end rot and was removed from the plant.
Blossom End Rot

Any internet search for “diseases of tomato fruits” will turn up lots of information on blossom end rot (BER), but you may find varying accounts of what exactly is causing this disease. In addition, this ailment is not actually a disease, but a physiological disorder, or a disorder related to the physical function of the plant.  It is not caused by a pathogen, as is the case with diseases.

The symptoms of BER are hard to miss, beginning as a tan or brown spot and expanding into a sunken, dark-colored and often leathery area of rot that typically ruins most of the fruit. This rot develops on the blossom end of the fruit, or the end opposite of the stem, where the flower was once attached.  Following the initial development of the “rot”, fungi and bacteria will often move in to cause further tissue decay, ruining the fruit.


Unfortunately, once the brown or black end on the fruit appears, it's too late, and these fruits need to be removed so they don’t draw any additional plant resources. There is no way to reverse or slow the development of this condition once it begins.

BER can also affect peppers, squash, eggplant, and watermelon. Certain tomatoes are more susceptible, with the larger-fruited varieties having a higher incidence of BER. Tomatoes with longer fruits, such as ‘Roma,’ have also shown higher susceptibility than those with more round fruits.

The mechanisms that cause BER are poorly understood, but most believe the condition relates to calcium levels in the developing fruit. In central Illinois, calcium is typically abundant in soils. However, the uptake of this soil macronutrient in tomato plants can be tricky and is tied to various environmental factors. 

Essentially, the uptake of calcium is dependent on the active transpiration of leaves. Recall that transpiration is the process by which leaves wick moisture (and nutrients) from the soil by expelling moisture through stomatal openings in leaves. Any environmental stress, such as too much or too little soil moisture that affects transpiration, can impact calcium uptake. Other factors such as soil salinity (affected by fertilizer application), humidity levels, and ambient temperature during fruit development have all been shown to affect calcium uptake and transport to developing fruits.

Some researchers have identified calcium deficiency as a symptom of BER instead of a cause. In these cases, researchers noted that fruits had adequate calcium levels early in development and lower levels after the onset of BER.   

Regardless of the exact cause, there are some recommendations you can try to prevent BER. First, avoid overfertilization and use ammonium-based fertilizers (ammonium interferes with calcium uptake). Another option is to select varieties less prone to BER, such as cherry tomatoes and more round-shaped fruit varieties.  

However, the most effective recommendation is to provide consistent soil moisture, especially during the early stages of fruit development. Avoid large swings in soil moisture by watering deeply (as opposed to frequent, shallow watering) and providing at least one inch of water per week. If hot, dry weather is predicted, water your plants in advance. Mulch can help greatly regulate large swings in soil moisture, adding yet another benefit to the long list we can attribute to mulching.

Harvesting Recommendations

To conclude this discussion of common tomato problems, I’d like to talk briefly about harvesting as we get quite a few questions about how and when to harvest tomatoes for optimal fruit conditions.  The highest quality tomatoes are ripened on the vine when average daily temperatures are about 75°F.  Harvest fruits when they are firm and fully colored and do not refrigerate.

As temperatures rise, the softening process is accelerated, and color development is slowed. Once the hot weather of July and August sets in, it pays to harvest tomatoes every day or two as new fruits have started to develop color.  The ripening process can then be completed indoors under more optimal temperatures (70-75°F).


Adams, P and  Ho, LC. 1993. Effects of environment on the uptake and distribution of calcium in tomato and on the incidence of blossom-end rot. Plant and Soil 154, 127–132.

Adams, P. 1991. Effect of diurnal fluctuations in humidity on the accumulation of nutrients in the leaves of tomato (Lycopersicon esculentum). J. Horticulture Science 66, 545–550.

Colebrook, EH et al. 2014. The role of gibberellin signaling in plant response to abiotic stress.  Journal of Experimental Biology 217(1), 67-75.

Chaerani, R and Voorrips, RE. 2006. Tomato early blight (Alternaria solani): the pathogen, genetics and breeding for resistance. Journal of General Plant Pathology 72, 335-347.

De Freitas, ST and Mitchum, EJ. 2012. Factors involved in fruit calcium deficiency disorders. Horticultural Review, 107-146.

Hagassou, D et al. 2019. Blossom end-rot in tomato (Lycopersicon esculentum L.): a multi-disciplinary overview of inducing factors and control strategies. Scientia Horticulturae 249, 49-58.

Saure, MC. 2014. Why calcium deficiency is not the cause of blossom-end rot in tomato and pepper fruit. Scientia Horticulturae 174, 151-154.