Preheat the oven to 350 degrees F.
Wash and remove stems from the whole mini bella mushrooms. Use a small spoon to remove the inside ribbing if needed to make more room for the stuffing. Arrange the mushrooms bottom side up on a parchment paper lined baking sheet.
Add shrimp, green onions, garlic cloves, jalapeno pepper, salt, pepper, and crushed red pepper flakes (optional) in a food processor. Pulse until everything is chopped small, making sure not to process too much (avoid the mixture becoming pureed).
Place the softened cream cheese into a small/medium bowl. Add the shrimp mixture and gently combine until no large chunks of cream cheese remain and everything is incorporated.
Spoon the mixture into the mushroom caps. A 1/2 tablespoon works well as a scoop, using more or less for the mushrooms depending on size. Fill the mushroom with a small heap on top, but avoid overfilling as the mixture may fall out as they bake.
Sprinkle each mushroom with fresh shredded parmesan cheese.
Bake at 350 for 15 minutes. Place under the broiler on high for 2-3 minutes until the tops are golden brown.