Preheat your oven to 400°F (200°C). Line a large baking sheet with parchment paper for easy cleanup.

Gently clean the mushrooms with a damp paper towel. Carefully snap off the stems. Finely chop the stems and set them aside; you will use these in the filling.

In a medium bowl, toss the mushroom caps with olive oil, salt, and pepper until evenly coated. Arrange the mushroom caps, cavity-side up, on the prepared baking sheet.

Heat a large skillet over medium-high heat. Add the Italian sausage and chopped yellow onion. Cook, breaking up the sausage with a spoon, for 5-7 minutes until the sausage is browned and the onion is soft. Drain any excess grease.

Add the minced garlic and the reserved chopped mushroom stems to the skillet. Cook for another 2-3 minutes until the garlic is fragrant and the mushroom stems are tender.

Remove the skillet from the heat. In a large mixing bowl, combine the cooked sausage mixture with the softened cream cheese, panko breadcrumbs, 1/4 cup Parmesan cheese, chopped cranberries, chopped pecans, parsley, dried thyme, and optional red pepper flakes. Stir until everything is well combined.

Using a small spoon, generously mound the filling into each mushroom cap. Sprinkle the tops with a little extra grated Parmesan cheese.

Bake for 15-20 minutes, or until the mushrooms are tender and the filling is golden brown and bubbly.

Let the stuffed mushrooms cool for a few minutes before serving. Garnish with fresh chopped parsley and serve warm.