What It Means If You See These Holes in Tomatoes!
If you’ve ever gone to pick a ripe, red tomato—whether from your backyard garden or the grocery store—only to discover tiny holes in the skin, you know that sinking feeling. It’s frustrating. You work hard tending plants or choosing fresh produce, and then nature decides to poke holes—literally—in your reward. But those little imperfections tell a story. Understanding what causes them can save your future harvests and keep your tomatoes safe to eat.
Let’s break down what’s really happening when tomatoes develop holes, what it means for your crop, and what you can do to prevent it.
Most often, holes in tomatoes are the calling card of pests. A few notorious culprits show up again and again: tomato hornworms, stink bugs, and various beetles. Each pest leaves a slightly different signature. Hornworms chew large, obvious holes and may leave droppings on nearby leaves. Stink bugs puncture the skin with their needle-like mouthparts, creating tiny, shallow wounds that later expand into sunken spots. Beetles, particularly flea beetles or fruitworms, prefer to burrow, leaving neat round entry points that quickly rot if untreated.
Then there are the uninvited guests from outside your garden bed—birds and squirrels. Birds tend to peck once or twice, usually out of curiosity or to quench thirst on a hot day. You’ll see small, triangular holes where their beaks struck. Squirrels, on the other hand, aren’t nearly so polite. They bite straight through the fruit, often leaving a half-eaten tomato dangling on the vine. If the damage looks like someone took a bite, you’re not dealing with insects—you’re feeding the wildlife.
Occasionally, holes appear for reasons unrelated to pests. Environmental stress can distort a tomato’s development. “Catfacing,” for example, is a deformity caused by temperature fluctuations during the flowering stage. The result is puckered scars and crevices that look like wounds. Another internal issue, blossom-end rot, begins at the bottom of the fruit and spreads upward, sometimes creating soft sunken spots that rupture over time. These aren’t caused by bugs at all, but by inconsistent watering or calcium deficiency in the soil.
So, can you eat a tomato that has a hole in it? The short answer: sometimes, yes—but use your senses and common sense. If the hole is small, clean, and there’s no mold, oozing, or sour smell, the tomato is probably still safe. Slice off the damaged portion with a clean knife and inspect the inside. If the flesh looks firm and fresh, go ahead and use it for sauce, salad, or sandwiches. However, if the tomato smells foul, feels slimy, or has mold growing near the hole, toss it. Once a pest or fungus gets inside, spoilage spreads fast.
Prevention, as always, is better than reaction. Protecting your tomato plants starts with vigilance. Walk your garden daily if you can. Look under the leaves and around the stems for signs of chewing or droppings. Hornworms, for example, blend in perfectly with tomato leaves until you look closely—they can reach the length of your finger and devour a plant overnight. If you find one, remove it manually and drop it into a bucket of soapy water.
Consistency is key in watering. Irregular moisture—drought followed by heavy watering—stresses plants and causes the fruit to crack or split. Those cracks become weak points where insects or fungi enter. Deep, even watering at the base of the plant keeps soil moisture stable and helps prevent this issue.
Netting or lightweight garden fabric can keep birds and squirrels at bay. Some gardeners swear by reflective tape or old CDs hanging from strings to scare off curious animals. Another natural defense is companion planting. Basil, marigolds, and garlic all help deter pests with their strong scent while attracting pollinators. Plus, they make your garden smell incredible.
Maintaining a clean garden bed also matters. Fallen fruit, dead leaves, and weeds create a buffet for insects and rodents. Regularly clear debris and compost any spoiled produce far from your active garden. The less temptation around, the fewer problems you’ll face.
Chemical pesticides are an option, but many home gardeners prefer natural methods. Neem oil, insecticidal soap, or homemade garlic sprays can control infestations without harming bees or beneficial insects. Always follow label directions carefully, especially when spraying near edible fruit.
If you grow tomatoes in containers, remember that soil nutrients deplete faster. Refresh your potting mix each season or supplement with compost. Proper nutrition strengthens the plant’s defenses, making it less attractive to pests.
Now, what should you do if you discover a hole in a tomato after harvesting? First, isolate it. Don’t let damaged fruit sit with healthy ones, since bacteria can spread quickly through contact. Inspect the hole. Is it clean and dry, or is there webbing, black mold, or small larvae? If it’s the latter, dispose of the tomato immediately and check nearby fruits. Wipe the area around your harvest basket with a diluted vinegar solution to prevent contamination.
Sometimes, you might notice holes while washing store-bought tomatoes. In that case, assume it’s from handling or transport damage rather than pests. Still, inspect and cut away any suspicious sections before eating.
Here’s a quick checklist to help you troubleshoot and prevent holes in tomatoes:
Inspect daily. Look for chew marks, frass (insect droppings), or discoloration.
Water evenly. Avoid letting plants dry out completely between waterings.
Prune properly. Air circulation keeps the foliage dry and discourages pests.
Use deterrents. Netting, marigolds, and reflective objects can protect fruit.
Keep it clean. Remove fallen tomatoes and weeds that harbor insects.
Rotate crops. Don’t plant tomatoes in the same spot year after year; soil pests linger.
A well-kept garden rewards patience. The difference between frustration and a flawless harvest often comes down to paying attention before problems escalate. A hole in a tomato isn’t just damage—it’s information. It tells you something about what’s happening in your garden: too much moisture, not enough nutrients, or visitors who love tomatoes as much as you do.
The good news? Once you know the cause, you can fix it. Most pest problems can be managed naturally. Environmental issues can be stabilized with steady watering and mulching. Birds and squirrels can be discouraged without traps or chemicals. A little consistency, a little observation, and your plants will repay you tenfold.
So, next time you find a tomato with a hole, don’t immediately throw it out in frustration. Take a closer look. You might learn something about your garden’s ecosystem—what it needs, what it’s attracting, and how it’s balancing itself. And if the tomato’s still good inside? Slice it, season it, and enjoy it proudly. After all, a home-grown tomato, even with a scar or two, still tastes better than anything from a store shelf.
Tomatoes might be high-maintenance, but they’re worth every bit of care. A few simple habits—watching, watering, and protecting—can turn your harvest from a casualty of pests into the centerpiece of your next meal. Those little holes aren’t the end of the story; they’re just reminders that even in the garden, perfection isn’t the goal—resilience is.