Preheat your oven to 400 degrees F and line a large baking sheet with parchment paper. Cut each jalapeño in half lengthwise and use a small spoon to scoop out the seeds and membranes. Wear gloves if you have sensitive skin.
In a medium bowl, mix together the softened cream cheese, shredded cheddar, crumbled bacon, garlic powder, smoked paprika, and salt until well combined.
Fill each jalapeño half generously with the cream cheese mixture, using a spoon or small spatula to mound it slightly above the pepper.
Set up a breading station with three shallow dishes. Place the gluten free flour in the first, beaten eggs in the second, and gluten free panko breadcrumbs in the third.
Take each stuffed jalapeño and dip the filling side into the flour, then into the egg, and finally press it into the panko breadcrumbs to coat the top and sides.
Place the breaded poppers filling side up on the prepared baking sheet. Spray the tops generously with cooking spray. This step is crucial for getting that crispy golden crust.
Bake for 20 to 22 minutes until the breadcrumb coating is deep golden brown and the peppers are tender. Let them cool for 5 minutes before serving. They are incredibly hot inside right out of the oven.