Tomato Harvest-Time Troubles

By Ashley Gaden, Master Gardener Intern

Tomatoes. Gardeners love them. But what we don’t love is coming across something unexpected, unattractive and utterly unwanted on our tomatoes after waiting most of the summer for them. From cracks and discolouration to rot and pest damage, tomatoes seem particularly vulnerable to a whole suite of problems.

Awareness and prevention will go a long way to maintaining the literal fruits of your labour. Here we’ll review some of the most common tomato fruit disorders and best practices to prevent or reduce their occurrence.

Non-living (abiotic) disorders

Sunscald (or sunburn or scorch) presents itself as a yellow or cream-coloured spot on a tomato that eventually whitens, blisters and softens or becomes papery, becoming susceptible to rot. Sunscald typically affects green tomatoes. This affliction is caused by too much sun exposure to the fruits, such as when tomato leaves and stems are pruned or if the plant becomes diseased and leaves fall off. Contrary to popular belief, tomato fruits do not need direct sunlight to ripen, and it actually slows down or stops the ripening process. Prune plants without removing all shade cover from leaves to blossoms/fruits.

Sunscald superinfected with fruit rot.
Typical papery sunscald lesion on a bell pepper.

Tomatoes can get cracks in their skin that radiate from the stem downwards or that circle the stem. A burst of water after a dry spell can cause tomatoes to grow too fast for their skin (think water balloon rupture). Too much fertilizer can also be a culprit. Using mulch can help the soil retain moisture during dry spells. Harvest tomatoes with cracks before fungi and bacteria take over the fruit.

Blossom end rot is a black spot or sunken bruise at the blossom end (bottom) of the tomato. This occurs when the plant is unable to absorb enough calcium. In prairie soils, this is a problem when there are uneven levels of moisture in the soil, which hinders nutrient uptake through plant roots. The conditions can be prevented by watering regularly. The University of Saskatchewan recommends 2.5cm water per week. Mulch also helps retain soil moisture. If growing in potting soil, use compost or fertilizer that contains calcium. Rotate your tomato plants annually and do not plant in the same area for a minimum of three years.

Blotchy or uneven ripening when temperatures are below 16 degrees C or above 29 degrees C (the ideal temperature for fruit ripening is between 21-24 degrees C), if there is a potassium or other nutrient deficiency, or if the tomato is growing in compacted or very wet soil, which makes nutrient uptake difficult for the plant’s roots. Grow tomatoes in well-drained soil and rotate crops on annual basis. If growing in a container with potting soil, use new potting soil. Mulch reduces soil compaction.

Yellow shoulder is a yellowing and hardening of the fruit around the stem, which can extend to inside the fruit. While the exact cause is unknown, yellow shoulder is a symptom likened to very high temperatures during ripening, and not enough potassium or organic matter in the soil. Acidic soils can also be an issue. Select varieties less prone to yellow shoulder and also consider testing your soil to see what, if any, amendments are needed.

Living (biotic) disorders

Fungi mould and rot fruit rot. Well-known culprits are Botrytis sp. and Colletotrichum coccoides. The latter species causes anthracnose, a fungal disease that starts as a black, flat spot on a ripe tomato and develops a ring or series of rings around it up to half an inch in diameter. The interior blackens with mold. Early and late blight, which are usually associated with potatoes, can also strike tomatoes. Whereas early blight (Alternaria solanis), a more common disease of late summer in Manitoba, rarely affects the fruit, late blight (Phytophthora infestans), a less common disease in prairie summers, can wipe out the entire plant. The first signs of both early and late blight occur as lesions on the leaves.


Bacterial infections generally appear as tiny spots on tomatoes. Bacterial speck causes black spotted bumps with white centres. Bacterial canker resembles small white spots with tiny black specks that strike ripe tomatoes. Do not eat tomatoes with bacterial infections.

Fungal and bacterial disease can strike when the plant is wet for a long time or there is not enough air circulation. The sites of plant injury (e.g., hail, wind-damage, blossom end rot, sunscald, cracks) can also be entry points for these culprits.

Prevention begins with using seeds from reputable sources and using disease-resistant varieties. The next consideration is the above-ground moisture level. Water plants early in the day so they can dry off in the sun and adequately space plants to improve air circulation and drying. Preferably water the base of the plant. If you water the whole plant, avoid handling the foliage while it is wet to prevent spreading spores. Get tomatoes off the ground by supporting vertical growth, such as by staking or using a trellis. Mulch also helps to reduce soil splash-up and spread of diseases. Don’t allow tomatoes to become over ripe on the vine.

If you know some of your plants are infected, disinfect garden tools between crops. Disinfecting tools is also generally recommended for after harvest or in spring, or when working between different gardens. See the University of Minnesota Extension’s Clean and disinfect gardening tools and containers webpage for more information. Remove and discard (not compost) or destroy infected plant material from the garden.

Insect damage

Tomato hornworms (the larvae of sphinx moths) can and will eat tomato fruits but usually forage on the foliage. They will bore a hole through the tomato fruit. These large caterpillars can be removed by hand.

Stink bugs suck out the juice of mature or immature tomato fruits, resulting in a symptom called “cloudy spot” that presents as light-yellow blotches on the exterior. This nuisance becomes more visible when tomatoes turn red. Gardeners can shake the plant above a tray to collect and discard the adult and nymph stages to try to control numbers. A preventative measure is to control weeds in and around the garden that could stage as overwintering locations for the pests.

Cloudy spot – Stinkbug Damage


An odd-looking tomato here and there is not a cause for alarm as it is still perfectly edible. “Catfacing” occurs on the blossom end (bottom) of the tomato fruit and is the result of how the flower developed (see above photo). This could be a result of how the flower was pollinated or conditions during fruit development, such as an abundance of nitrogen, very hot or cold temperatures, or alternating extreme soil moisture conditions. Zippering is a term used to describe a scar on the blossom end, which is what happens when the blossom’s anther becomes attached to the developing and growing fruit.

Catfacing and Zippering

Looking ahead

With projected hotter and drier summers sprinkled with intense downpours in the prairies, it’s never too early to start using moisture-conserving gardening practices. Mulching, along with consistent watering, conservative pruning and adequate nutrient levels, will prevent or reduce many of the disorders discussed above. Your tomatoes will love it and so will you.

For information on successfully growing healthy tomatoes, please read Lenore Linton’s articles in the Manitoba Master Gardener Association’s Newsletter: Growing Tomatoes – Part 1 of 2 and Growing Tomatoes – Part 2 of 2, from Transplants to Harvest.

More photos of the tomato fruit problems described can be found in A visual Guide – Problems of Tomato Fruit published by the Missouri Botanical Garden, William T. Kemper Center for Home Gardening

Photos: Yellow Shoulder, Catfacing and Zippering, Sunscald superinfected with fruit rot, fruit cracks by Lenore Linton.

Photos: Anthracnose, Cloudy Spot- Stinkbug Damage, Concentric and Radial Cracks by Lisa Renner


Missouri Botanical Garden. Tomato Diseases and Disorders. William T. Kemper Centre for Home Gardening.
Missouri Botanical Garden. 2012. A Visual Guide – Problems of Tomato Fruit. William T. Kemper Centre for Home Gardening.
Missouri Botanical Garden. Tomatoes. William T. Kemper Centre for Home Gardening.
Schuh, M. 2022. Early blight in tomato and potato. University of Minnesota Extension.
Schuh, M. 2021. Cracks, Rots, and Tough Spots: Tomato Quality Issues. University of Minnesota Extension.
University of California Agriculture and Natural Sciences. Stink Bugs. Statewide Integrated Pest Management Program.
University of Massachusetts. Tomato, Physiological Ripening Disorders. UMass Extension Vegetable Progam, Center for Agriculture Food and the Environment.
University of Saskatchewan. Tomatoes. Gardening at USask. College of Agriculture and Bioresources.
Voyle, G. 2015. Trouble in Tomatoland: When Tomatoes Are Not Attractive. Michigan State University Extension.
Weisenhorn, J. 2020. Clean and Disinfect Gardening Tools and Containers. University of Minnesota Extension.
Yi. L. 2013. Anthracnose of Tomato. The Connecticut Agricultural Experiment Station. Pp. 1-2.

Published: September 2022