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11 Pruning Mistakes That Can Affect Your Garden Tomato Yield

Kuzey

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Different tomatoes in baskets near the greenhouse. Harvesting tomatoes.

Tomatoes are a crowd favorite in the garden for beginners and seasoned gardeners alike. At first glance, growing them seems simple, but for a healthy and abundant harvest, certain care techniques are important.

One of the key techniques is pruning, which helps direct the plant’s energy where you want it (growing those ripe, juicy tomatoes!). When done correctly, pruning results in plentiful fruit, while keeping the plant strong and resilient. However, if done incorrectly, it can drastically reduce yield.

Let’s look at the most common mistakes made when pruning tomatoes. Each one is explained in detail with practical advice. We sourced and confirmed our advice from trusted University extensions University of Wisconsin and Iowa State University. We also included a few ancillary recommendations based on our own experiences (personal and from our Facebook community) to give you well-rounded ideas to support your tomato plants.

1. Over-Pruning the Plant​


Pruning Tomato


One of the most common mistakes is removing too many leaves and stems. Without enough foliage, the tomato plant loses its ability to photosynthesize effectively. This means it cannot produce enough energy to develop and ripen fruit properly. As a result, tomatoes may end up smaller and less flavorful. Over-pruning also increases the risk of sunscald, as the fruits remain directly exposed to sunlight.

Proper pruning means balancing between removing excess growth and leaving what the plant needs. The goal is to ensure good airflow and light penetration while maintaining enough leaves for food production. Experienced gardeners typically keep the main stem and several strong branches.

Pro tip: Pruning should be done gradually, never all at once. This gives the plant time to adjust and continue growing normally.

2. Not Pruning at All​

Newly planted tomato plant in a tomato cage in a home garden

Image Credit: Shutterstock.


Many beginners believe tomatoes should be left to grow freely. This leads to an overcrowded plant with dense foliage. When there are too many stems and leaves, air cannot circulate properly. That creates the perfect environment for diseases such as blight. In addition, the plant uses more energy in its leaves instead of its fruit.

Proper pruning opens space within the plant. Sunlight can reach flowers and fruits more effectively. Better air circulation reduces the risk of fungal diseases. Fruits also ripen more evenly and quickly. Without pruning, yields are usually lower and of poorer quality.

3. Pruning at the Wrong Time of Day​

Close-up of tomato plant and hands with pruning shears shaping bush

Image Credit: Shutterstock.


Another mistake is pruning during the hottest part of the day. Some gardeners theorize that putting the plant under strong sunlight causes wounds to heal more slowly. This increases the risk of infection and tissue damage. The plant experiences more stress. As a result, growth slows down and yield decreases.

The best time for pruning is in the morning. At this time, the plant is refreshed and recovers more quickly. Cuts made early in the day have enough time to dry and seal. This reduces the risk of nighttime infections when humidity rises. Morning pruning helps maintain plant health and maximize productivity.

Note: This is a theory that is often shared and makes plausible sense, but it is not strongly supported by trusted gardening sites at this time.

4. Removing Healthy Leaves Near Fruit Clusters​

Close-up of tomato plant and hands with pruning shears shaping plant

Image Credit: Shutterstock.


Some gardeners think that removing leaves will make fruits ripen faster. However, leaves near clusters are the main source of energy for those tomatoes. If removed too early, the fruits remain smaller and less tasty. The plant then draws energy from other parts. The result is uneven ripening.

Instead of removing all leaves, keep some healthy ones close to fruit clusters. These leaves feed the flowers and developing fruit. Once tomatoes start turning red, you can gradually remove some foliage. This way, fruits receive both sunlight and nutrients. The result is larger, juicier, and better-flavored tomatoes.

Note: This is another anecdotal observation (and theory) from home gardeners that we found in our Facebook groups, and is not directly supported.

5. Leaving Too Many Suckers​

hand picking pruning sucker off tomato plant

Image Credit: Shutterstock.


Suckers are small shoots that grow in the leaf axils. If left unchecked, they turn the plant into a tangled mess. This leads to overcrowding, a lack of light, and lower yields. Energy is spread across too many stems. The result is smaller, weaker fruit.

It’s best to remove suckers regularly while they’re still small. At that stage, the plant hasn’t wasted much energy on them. Not all suckers need to be removed, though (leave a few to support growth). The key is a balance between foliage and fruit production. This way, tomatoes get enough nutrients for healthy development.

6. Using Dirty or Dull Tools​

Person's hands sanitizing pruning shears blades with alcohol swab

Image Credit: Shutterstock.


Another serious mistake is pruning with dirty or blunt tools. Dull shears tear instead of cutting cleanly. Wounds heal more slowly and provide entry points for disease. Viruses and fungi easily spread from one plant to another this way. The plant becomes weakened and less productive.

Before each pruning session, disinfect your tools. Wiping them with alcohol or a bleach solution is enough. Sharp tools create clean cuts that heal quickly. This helps the plant stay strong and resistant. Such a simple habit can prevent major losses in yield.

7. Treating Determinate and Indeterminate Varieties the Same​

Growing tomato plants tied to wood supporting stakes. Green, organic agriculture concept background

Image Credit: Shutterstock.


There is a big difference between determinate (bushy) and indeterminate (vining) tomatoes. A common mistake is pruning both types the same way. Determinate varieties should not be heavily pruned, as this reduces fruit production. Indeterminate varieties, however, require regular sucker removal. Without it, they overgrow and tangle.

Recognizing the difference is crucial for yield. Bush varieties naturally stop growing and should remain fuller. Vining types should be tied to stakes and shaped continuously. This ensures good airflow and higher fruit production per stem. Pruning incorrectly can easily cut harvests in half.

8. Cutting Too Close to the Main Stem​

Tomatoes damaged by pest or bug in tomato plantation or field. Tomato (Solanum lycopersicum and Lycopersicon esculentum) crop damaged by pest.

Image Credit: Shutterstock.


Some gardeners mistakenly cut suckers flush against the main stem. This often damages the main stem itself. Such wounds heal slowly and open the door to infection. This can cause rot and partial plant failure. As a result, yield drops significantly.

The proper technique is to leave a small stub behind. This prevents damage to the main stem. These small stubs dry out and fall off naturally. The plant remains strong and protected. This simple practice keeps tomatoes healthy all season long.

9. Ignoring Lower Leaves​

Disease of tomatoes. Blossom end rot on the fruit. Damaged red tomato in the farmer hand. Close-up. Crop problems. Blurred agricultural background. Low key

Image Credit: Shutterstock.


Lower leaves often touch the soil. This isn’t ideal because soil contains fungi and bacteria. When rain or irrigation splashes soil onto leaves, disease spreads easily. If lower leaves aren’t removed, infections quickly move up the plant. Fruits are damaged, and the yield decreases.

Regular removal of lower leaves is essential. Ideally, clear the stem up to the first flower cluster. This reduces soil contact and disease risk. The plant grows healthier and stronger. It’s one of the most important preventative measures in tomato care.

10. Pruning in Wet Conditions​

Hands of a girl with a watering hose close-up. The farmer's wife waters the tomatoes. The concept of caring for agricultural plants and harvesting.

Image Credit: Shutterstock.


Many gardeners prune tomatoes right after rain or watering. This is a mistake because wet wounds heal slowly. Moist leaves are perfect for fungal growth. Infections spread much faster on damp plants. Yield can drop drastically as a result.

The ideal time to prune is during dry weather. The plant then has the best chance to recover quickly. Try to avoid high humidity when cutting. If pruning is done when leaves are dry, the risk of disease is minimal. This rule applies to all tomato varieties.

Note: This advice isn’t well-documented by Master Gardeners, but it makes practical sense nonetheless.

11. Neglecting Continuous Pruning​

Close-up pruner in hand. Cuts ripe red tomatoes. Cutting tomatoes. Using a garden tool

Image Credit: Shutterstock.


Another common mistake is pruning only once during the season. Tomatoes grow fast and constantly produce new suckers. If ignored, the plant quickly becomes overcrowded again. This brings back the same problems of excess foliage and poor fruiting. Continuous pruning is essential.

It’s best to check plants at least once a week. This way, new suckers can be removed while still small. Minor cuts heal quickly and don’t stress the plant. If pruning is delayed, the work becomes harder and more harmful. Consistency is the key to strong plants and high yields.
 
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