Thank you for reaching out to ask2.extension.

The most likely cause of your bell pepper holes is some sort of insect invasion. There are unfortunately a fairly large number of insects that attack peppers. Most common are the pepper maggot and corn borer. Less common are the tomato fruitworm , beet army worm and a variety of caterpillars, aphids and thrip.

Controlling insect infestations is an ongoing battle. You could try an organic pesticide:

One teaspoon of vegetable oil
One teaspoon of dishwashing liquid
One cup of water

Spray the plant thoroughly, then respray after a few hours to remove the soap. Wash your peppers well before eating them.  I’d try this now even if you’re not seeing insects, because they are there.

With regard to the safety of your fruit, first cut out the damaged area, then carefully cut into the fruit making sure that there is no insect activity inside. Rinse out the pepper and it should be good to go. It’s up to you if you’re ok with eating the good part.

Finally, the best time to combat insect infestations is by catching them early. Next season, check your plants frequently (including under the leaves) and use an insecticide if you see any bugs or caterpillars. Early detection and prevention is a much the most effective weapon against our bug issues.

I hope this helps.