Preheat the oven to 425 degrees F. Line a baking sheet with foil.
Add the cream cheese, smoked Gouda, Cheddar, chives, lime zest, lime juice, salt and pepper to a medium bowl. Mix thoroughly until evenly combined.
Divide the cream cheese mixture between the jalapeño halves, pressing to fill all the way to the top edge.
Wrap a piece of bacon around each stuffed jalapeño so the ends of the bacon lie underneath. Place the wrapped jalapeños, stuffed-side up, on the prepared baking sheet. Bake until the bacon is crispy and the cheese mixture is just beginning to bubble out from the top and bottom of the jalapeños, 16 to 18 minutes. Remove from the oven and let cool 10 minutes before serving.