If you’ve ever reached out to pick a plump, sun-warmed tomato—whether from your own backyard garden or the grocery store shelf—only to notice tiny holes piercing the skin, you probably know that disappointing moment all too well. It’s frustrating. After all the time spent watering, pruning, and nurturing your plants—or carefully selecting the best produce—nature suddenly seems to sabotage your efforts. But those small imperfections aren’t random. They tell a story about what’s happening in your garden, and understanding that story can help you protect future harvests and still enjoy safe, delicious tomatoes.

Let’s take a closer look at why tomatoes develop holes, what these marks really mean, and how you can stop them from ruining your next crop

More often than not, holes in tomatoes are the unmistakable signature of pests. A few usual suspects appear time and time again: tomato hornworms, stink bugs, and different types of beetles. Each of these invaders leaves behind a unique pattern of destruction. Hornworms, for instance, chew large, ragged holes and often leave behind dark droppings on the leaves. Stink bugs pierce the fruit with their needle-like mouthparts, leaving tiny punctures that later grow into sunken, discolored patches. Beetles—especially flea beetles or fruitworms—are more surgical in their approach, boring neat, round entry holes that can quickly become infected and rot if not treated promptly.

But not all offenders crawl or buzz. Sometimes, the culprits are feathered or furry. Birds are notorious for pecking tomatoes once or twice—often just to quench their thirst on a hot day—leaving behind small, triangular punctures. Squirrels, however, are far less subtle. 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 battling insects—you’re running a wildlife buffet.

In other cases, holes form for reasons entirely unrelated to pests. Environmental stress can warp a tomato’s growth and appearance. One example is “catfacing,” a deformity caused by extreme temperature changes during flowering, resulting in puckered scars and open crevices that look like wounds. Another issue, blossom-end rot, begins at the base of the fruit due to irregular watering or a calcium deficiency. It creates dark, soft spots that can rupture as the fruit matures. These problems come from the plant’s environment, not from insects—and they’re a reminder that balance is everything in gardening.

So what should you do if your tomato has a hole? The answer depends on what you find. If the damage 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. But if it smells bad, oozes liquid, or shows mold near the hole, it’s best to discard it. Once pests or fungi get inside, decay spreads quickly.

Of course, prevention is the best cure. Keeping your plants healthy starts with observation. Check your garden daily—especially under leaves and along stems—for chewing marks or droppings. Hornworms, for instance, can blend perfectly with tomato leaves and grow as long as your finger, capable of stripping a plant bare overnight. If you spot one, remove it by hand and drop it into soapy water.

Steady watering is also essential. When plants swing between drought and heavy watering, the sudden change can cause fruit to crack or split, creating weak points where pests or mold enter. Consistent, deep watering at the base of the plant helps keep the soil evenly moist and prevents this issue.

If birds or squirrels are your problem, try 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 even 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 wonderful.

Cleanliness in the garden goes a long way. Fallen fruit, dead leaves, and tall weeds invite insects and rodents to move in. Clear away debris regularly and compost spoiled fruit away from your active beds. The tidier the area, the fewer pests you’ll have to deal with.

Some gardeners reach for pesticides, but there are safer, natural alternatives. Neem oil, insecticidal soap, and homemade garlic sprays can manage infestations effectively without harming bees or beneficial insects. Just be sure to follow 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 strong, well-fed plant is naturally more resistant to pests and disease.

When you discover a damaged tomato during harvest, isolate it right away. Don’t store it with healthy ones, since bacteria can spread through contact. Inspect the damage closely. If you see black mold, silk-like webbing, or tiny larvae, throw it out and check nearby fruits. Wipe down your harvesting tools and baskets with a mild vinegar solution to prevent contamination.

Even store-bought tomatoes can show small holes, usually from handling or transport damage. These are generally harmless, but it’s still wise to wash and cut away any questionable areas before eating.

Here’s a quick reference checklist to help you prevent holes in your tomatoes:

Inspect 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.

Keep it clean—remove debris and fallen fruit promptly.

Rotate crops each season to prevent soil-borne pests from multiplying.

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—too much heat, too little calcium, or a few 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 next time you find a tomato with a hole, don’t get discouraged. Take a moment to inspect, learn, and adapt. Each 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 proudly. After all, even a scarred tomato grown with care tastes better than any perfect one from the store.

Tomatoes may demand care, but they repay it with unmatched flavor. Those little holes? They’re not flaws—they’re reminders that every garden, like every gardener, grows stronger through experience.