If you’ve ever reached out to pick a ripe, sun-warmed tomato—whether from your own garden or the grocery store shelf—only to notice small holes piercing the skin, you’re probably familiar with that disappointing moment. It’s frustrating. After all the time spent watering, pruning, and nurturing your plants—or carefully selecting the best produce—nature seems to undermine your efforts. But those small imperfections aren’t random; they’re clues that reveal what’s happening in your garden. Understanding what they mean can help you protect future harvests and still enjoy safe, delicious tomatoes.
Let’s take a closer look at why tomatoes develop holes, what those marks really mean, and how you can prevent them from ruining your next crop.
Why Do Tomatoes Develop Holes?
More often than not, holes in tomatoes are a telltale sign of pests. A few familiar culprits keep showing up: tomato hornworms, stink bugs, and various types of beetles. Each one leaves behind a distinct pattern of damage. Hornworms, for instance, create large, ragged holes and often leave dark droppings on the leaves. Stink bugs pierce the fruit with their needle-like mouthparts, leaving tiny punctures that eventually expand into sunken, discolored patches. Beetles, like flea beetles or fruitworms, are more precise, boring neat, round entry holes that can quickly become infected and rot if not dealt with promptly.
But not all offenders are insects. Sometimes, the culprits are feathered or furry. Birds are notorious for pecking at tomatoes, often just to quench their thirst on a hot day, leaving behind small, triangular punctures. Squirrels, on the other hand, are much more direct. They’ll bite straight into the fruit, leaving half-eaten tomatoes dangling from the vine like a taunt. If it looks like someone took a literal bite out of your tomato, you’re not fighting insects—you’re dealing with a wildlife buffet.
In some cases, holes develop for reasons unrelated to pests. Environmental stress can alter a tomato’s growth and appearance. For instance, “catfacing” occurs when extreme temperature fluctuations during flowering cause puckered scars and open crevices that resemble wounds. Another issue, blossom-end rot, begins at the base of the fruit due to inconsistent watering or a calcium deficiency. It creates dark, soft spots that can rupture as the fruit matures. These problems stem from the plant’s environment, not insects—and they’re a reminder that balance is key in gardening.
What to Do with a Damaged Tomato?
What should you do if you find a tomato with a hole? It depends on the severity and cause of the damage. If the hole is small, clean, and the tomato doesn’t smell sour or feel slimy, it’s usually safe to eat. Simply cut away the damaged area and inspect the inside. If the flesh is firm, juicy, and unspoiled, go ahead and use it in your next salad, sauce, or sandwich. However, if the tomato smells bad, oozes liquid, or shows signs of mold near the hole, it’s best to discard it. Once pests or fungi enter, decay spreads quickly.
Prevention is Key
Of course, prevention is the best solution. Keeping your plants healthy begins with consistent observation. Check your garden daily—especially under leaves and along stems—for signs of chewing, droppings, or any damage. Hornworms, for instance, can blend perfectly with tomato leaves and grow as long as your finger, stripping a plant bare overnight. If you spot one, remove it by hand and drop it into soapy water.
Steady watering is also critical. Sudden changes between drought and heavy watering can cause fruit to crack or split, creating weak points where pests or mold can enter. Consistent, deep watering at the base of the plant helps maintain even moisture and prevents this issue.
If birds or squirrels are the problem, consider adding a barrier. Lightweight netting or floating row covers can keep them out, while reflective tape, aluminum foil, or old CDs strung between stakes can startle them away. You can also enlist nature’s help—companion plants like basil, marigolds, and garlic release strong scents that repel many pests while attracting pollinators. Plus, they make your garden look and smell fantastic.
Cleanliness in the garden is also essential. Fallen fruit, dead leaves, and overgrown weeds attract insects and rodents. Clear away debris regularly and compost spoiled fruit away from your active beds. The tidier your garden, the fewer pests you’ll have to deal with.
Some gardeners opt for pesticides, but there are safer, natural alternatives. Neem oil, insecticidal soap, and homemade garlic sprays can manage infestations without harming bees or beneficial insects. Just be sure to follow the instructions carefully, especially when treating plants that are already producing fruit.
If you grow tomatoes in pots or raised beds, remember that nutrients get used up faster in confined soil. Refresh your potting mix each season or mix in compost to replenish calcium and nitrogen. A well-fed plant is naturally more resistant to pests and disease.
What to Do When You Find a Damaged Tomato
When you discover a damaged tomato during harvest, isolate it immediately. Don’t store it with healthy tomatoes, as bacteria can spread through contact. Inspect the damage closely. If you find black mold, silk-like webbing, or tiny larvae, discard the tomato and check nearby fruits. Wipe down your harvesting tools and baskets with a mild vinegar solution to prevent contamination.
Even store-bought tomatoes can have small holes, typically due to handling or transport damage. While these are generally harmless, it’s still wise to wash and cut away any questionable areas before eating.
Quick Reference Checklist:
Inspect your plants daily for bite marks, droppings, or damaged leaves.
Water consistently to prevent splitting and stress.
Prune properly to improve airflow and reduce hiding spots for pests.
Use deterrents like netting, marigolds, or reflective tape to keep pests away.
Keep the garden clean—remove fallen fruit and debris regularly.
Rotate crops each season to prevent soil-borne pests from multiplying.
Conclusion: The Rewards of Patience
At the end of the day, gardening is a lesson in patience and observation. Every flaw in your harvest tells you something about your environment—whether it’s too much heat, too little calcium, or too many hungry visitors. The good news is that most of these problems have simple, natural fixes. A little consistency, a little attention, and your garden will thrive.
So, the next time you find a tomato with a hole, don’t get discouraged. Take a moment to inspect, learn, and adapt. Every imperfection teaches you more about your plants, your soil, and your ecosystem. And if the tomato still looks good inside? Slice it, season it, and enjoy it with pride. After all, even a scarred tomato grown with care tastes better than any perfect one from the store.
Tomatoes may require attention, but they repay that care with unmatched flavor. Those little holes? They’re not flaws—they’re reminders that every garden, like every gardener, grows stronger through experience.