Tomatoes are the crown jewel of backyard gardens. No vegetable gets planted with more anticipation or more heartbreak when things go wrong. If you’ve struggled to get a good tomato harvest—or you’re growing them for the first time—this guide is here to help you avoid five common mistakes and grow juicy, healthy tomatoes the Deep Roots way.
Mistake #1: Leaving the Lower Leaves On
One of the biggest mistakes gardeners make is leaving the lowest leaves on the tomato plant after it's been transplanted. These early leaves once served a purpose—helping the seedling break through the soil and photosynthesize—but once the plant grows taller, they become liabilities.
Rain and irrigation can splash soil up onto these bottom leaves, spreading fungal and bacterial diseases. By trimming the leaves below the first flower cluster, you dramatically reduce the risk of infection. This also improves airflow at the base, helping your tomato plant stay dry and disease-free.
Pro tip: If you’re planting tomatoes deep to encourage rooting along the stem (a great idea), trim the lower branches a few days before transplanting. That gives the stem time to heal and prevents infection from open wounds.
Mistake #2: Fertilizing the Wrong Way or Not Enough
Tomatoes are heavy feeders. Unlike forest ecosystems, vegetable gardens don’t replenish their nutrients naturally—everything the plants take from the soil must be put back by you.
Many gardeners under-fertilize or use low-quality fertilizers. At Deep Roots Project, we recommend a powerful, soil-friendly combination: worm castings and fish emulsion.
Why Deep Roots fertilizers work better. Most powdered fertilizers—especially the ones sold in bags at big-box stores—are manufactured from isolated nutrients. These quick-fix formulas may “green up” your plants fast, but they don’t feed the soil, and over time, your soil becomes depleted.
Worm castings are nature’s perfect slow-release fertilizer. Made by red wiggler worms from nutrient-dense organic matter, they’re packed with microbes that wake up your soil and help roots absorb nutrients better. They improve soil structure, water retention, and disease resistance—benefits that powdered fertilizers just can’t match.
Fish emulsion, especially cold-processed organic types, gives your tomatoes a gentle, balanced dose of nitrogen, phosphorus, and potassium. It’s also loaded with micro-nutrients and beneficial bacteria. When watered in every two weeks, it keeps your tomatoes growing strong without the harsh chemical burn of synthetic options.
Our Suggested Routine (Every Two Weeks):
• Top-dress each plant with ½ to 1 cup of worm castings.
• Water in with fish emulsion (about 2–3 tablespoons per gallon).
• Repeat every 14 days for happy, productive plants.
Want to go 100% organic? Great. Need to cut costs and mix in a bit of a commercial product? Fine. But always keep high-quality compost and natural fertilizers at the heart of your routine. Healthy soil = healthy tomatoes.
Mistake #3: Over-Pruning Tomato Plants
Pruning has become a trend among tomato growers—but many are doing too much. For determinate (bush) or dwarf varieties, never prune above the first flower cluster. These plants are pre-programmed to stop growing at a certain height. Over-pruning means fewer fruits.
For indeterminate tomatoes (which keep growing all season), it’s tempting to remove every sucker (the shoots that grow between the main stem and branches). But unless you're growing inside a greenhouse with 20-foot vertical space, this "single-stem" method will lower your yield. In a home garden, allow suckers to develop—especially ones low on the plant that your support structure can handle. More suckers = more flowers = more tomatoes.
Key takeaway: Prune for airflow and structure, not out of habit. If you can’t explain why you're pruning a certain branch, don't prune it.
Mistake #4: Planting Too Late in Warm Climates
If you live in a hot, humid region, timing is everything. Once daytime temps consistently hit 90°F and nights don’t dip below 70°F, tomato flowers won’t pollinate. Pollen becomes sticky, and flowers drop without forming fruit.
In cooler regions, gardeners are taught to wait until the danger of frost is well past. But in the South and other hot climates, waiting too long can mean a total harvest failure. Tomatoes should be planted early in spring, so they reach their peak flowering before the worst summer heat arrives.
If you're relocating from a northern state, adjust your timing expectations. Aim to plant tomatoes on the shoulder season—early enough to flower before the summer swelter.
Mistake #5: Believing the 'Full Sun' Myth
“Full sun” is a misleading term. While tomato seedlings love spring sunshine, intense summer sun stresses the plants, making them more vulnerable to disease and insect attack.
In their native tropical forests, tomatoes grow as sprawling vines under a canopy of dappled light. That’s why Deep Roots recommends 40% shade cloth during the summer.
Here's the winning formula:
• Let your tomatoes soak up the full sun in spring (April–May).
• Then, install shade cloth starting around Memorial Day to mimic their native light conditions.
This keeps your plants cool, reduces disease pressure, and extends your harvest by 45 to 60 days.
Final Thoughts on Tomato Mistakes
Whether you’re growing five tomato plants or fifty, mastering these five tips will set you up for success. Use Deep Roots Project’s organic fertilizers, plant at the right time, prune wisely, and protect your tomatoes with shade when the summer sun turns brutal.
Tomatoes may be the most beloved crop in the garden—but they’re also one of the trickiest. With a little knowledge and the right soil-building approach, your tomato patch can become the envy of the neighborhood.
The Tomato Pruning Debate
Pruning tomato plants has been a topic of debate among gardeners. Some claim that it increases yield, while others believe it's unnecessary. Scientific evidence does suggest that pruning can have specific benefits, but the extent of its impact on yield can vary based on factors like tomato variety, growing conditions, soil nutrients/microbes and pruning techniques.
Recent research has begun to challenge the long-held belief that pruning tomato plants invariably leads to better yields and healthier crops. While pruning can offer certain benefits, such as improved air circulation and disease prevention, studies suggest that its impact on yield and fruit quality may not be as significant as once thought.
Are Benefits of Pruning Tomatoes Just a Myth?
Pruning is not a myth, but its benefits can be specific to certain circumstances:
Indeterminate vs. Determinate Varieties: Pruning is more beneficial for indeterminate varieties that continue to grow and produce fruit throughout the season.
Disease Management: Improved air circulation from pruning can reduce the risk of fungal diseases.
Fruit Quality: Pruning can result in larger, higher-quality fruits.
However, for determinate varieties, which produce fruit in a shorter, more concentrated period, pruning is less critical and may not increase yield.
A Recent Science on Tomato Pruning
Studies collected by The Spruce suggest that while pruning can have specific benefits, such as disease prevention and plant manageability, it may not universally enhance yield or fruit quality. Home gardeners should consider factors like tomato variety, local climate, and available resources when deciding on pruning practices. For instance, determinate varieties often require minimal pruning, while indeterminate types may benefit from selective pruning to manage growth. Read full article by The Spruce “Should You Prune Out Tomato Suckers.”
The Spruce is committed to the quality and trustworthiness of their content and editorial processes. Their team of writers, editors, fact checkers, illustrators, photographers, and medical and financial professionals rigorously researches and reviews all content on an ongoing basis to ensure it is up to date, accurate, and puts the needs of their readers first. Learn more at The Spruce Content Integrity Promise
Customize Your Pruning Methods
In summary, pruning should be tailored to individual gardening contexts rather than applied as a one-size-fits-all solution. Understanding the specific needs of your tomato plants and observing their responses to pruning can lead to more informed and effective gardening practices.
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