Preheat the oven to 400 degrees and line a baking sheet with parchment paper or lightly oil a baking dish.
Carefully remove the stems from the mushrooms. They’re the bases of the stuffing so don’t throw them away! Trim around the mushroom opening if needed.
Mince the mushroom stems. Go as small as you can.
Heat the oil in a skillet over medium-high heat. Add the minced onion and a pinch of salt and cook for about 5 minutes, until the onion is fragrant and slightly brown.
Add the garlic, the mushrooms stems and a pinch of salt. Cook until the mushrooms are are very soft, about 10 more minutes. Mix in the red pepper flakes, and salt and pepper to taste.
Remove from the heat and mix in the breadcrumbs. If the mixture is too dry add a little water or stock. Add a tablespoon at a time, so you don’t water the mixture down too much. Gently fold in the parsley.
Stuff the mushroom caps with the stuffing and arrange on your baking sheet or pan. Bake until the mushrooms are tender and the stuffing is hot, about 20 minutes.
Top each mushroom with a dollop of pesto and garnish with a few grape tomato slices.