Start by halving your jalapeños lengthwise and carefully removing all seeds and white membranes using a small spoon or knife—this reduces heat and creates the perfect vessel for filling. While you're working on the peppers, cook the bacon in a skillet over medium-high heat until it's crispy, about 8-10 minutes. Once cooked, transfer the bacon to a paper towel-lined plate to drain, then crumble it into a small bowl once it's cool enough to handle.
In a medium bowl, combine the softened cream cheese with the shredded cheddar cheese, stirring until well blended. Add the chili powder, garlic powder, cumin, smoked paprika, lime juice, kosher salt, and freshly cracked black pepper, mixing thoroughly to ensure the spices are evenly distributed throughout the cheese. Fold in the crumbled bacon from Step 1 and the fresh cilantro—I like to reserve just a small pinch of cilantro for garnish to keep it bright and fresh-looking at the end.
Generously fill each jalapeño half with the cheese mixture from Step 2, packing it in firmly so it holds together during grilling. I find it helps to use a small spoon or piping bag to get the filling into the peppers evenly and without making a mess. Arrange the filled peppers on a clean plate, ready to go to the grill.
Preheat your grill to medium heat (around 350-400°F). Place the filled jalapeños skin-side down on the grill grates, being careful not to move them around too much to prevent the cheese from leaking out. Grill for 10-15 minutes, watching carefully until the peppers are charred and tender, and the cheese filling is hot and slightly melted on top. The skin should blister and blacken slightly, which adds a beautiful smoky flavor.
Transfer the grilled poppers to a serving platter and while they're still hot, sprinkle with the red pepper flakes and reserved fresh cilantro for color and a final burst of flavor. Serve immediately while the cheese is at its creamiest and the peppers are still warm.