Preheat your oven to 375°F and line a baking sheet with parchment paper. Cut the squash in half lengthwise and scoop out the pulp, leaving about 1/4 inch of squash around the edges. Place the squash halves on the baking sheet. Chop the scooped pulp into small pieces.
Melt 1 tablespoon butter in a skillet over medium-high heat. Add the chopped squash pulp, bell pepper, and onion. Cook for 3 minutes, stirring often, until softened. Add garlic, cumin, and salt; cook for 30 seconds more. Remove from heat and let cool slightly.
In a small bowl, stir together the panko breadcrumbs, remaining 1 tablespoon melted butter, and 1/3 cup of cheese. Set aside.
Stir the remaining 1/3 cup cheese into the cooled vegetable mixture. Spoon the filling into the squash shells and top with the breadcrumb mixture.
Place in the oven and bake for 20–25 minutes, until the topping is lightly browned.
Sprinkle with cilantro and serve warm.