Cook bacon in a large skillet over medium-high heat until browned. Drain on paper towels; crumble and set aside.
Preheat oven to 350°F (175°C). Coat a baking dish with cooking spray.
In the same skillet, heat olive oil over medium heat. Add chopped mushroom stems, jalapeño, and garlic. Cook, stirring often, until mushrooms release moisture and soften, about 10 mins.
Transfer mushroom mixture to a bowl. Stir in cream cheese, Cheddar cheese, and crumbled bacon. Season with salt and black pepper. Spoon cheese mixture generously into mushroom caps. Place caps in the prepared baking dish.
Bake until cheese starts to brown, 15 to 20 mins.
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