Preheat oven to 350 degrees and line a baking sheet with parchment paper. Cut peppers lengthwise and scoop out seeds.
Heat a skillet on medium heat and add in onions, mushrooms, oregano, garlic powder, thyme, salt and pepper. Sauté for 5-7 minutes. I use splashes of water to keep the veggies from sticking instead of adding oil. Then add in the pizza sauce, mixing it all together.
Scoop the mushroom mixture into each pepper on the baking sheet. Place them in the oven for 25 minutes. If you want to add a vegan cheese - take them out, cover with cheese and put back in the oven until it is melted, about 3-4 minutes.
Top with fresh basil or red pepper flakes and serve immediately. These are best enjoyed right away. I've had them a few hours later and they are still good, but the mixture can make the peppers get too soft if it sits too long. I'm not sure how well they would hold up the next day.