01 - Preheat oven to 400°F (200°C). Line a 12-cup muffin tin with paper liners or grease well.
02 - Cook elbow macaroni according to package directions until just al dente. Drain and set aside.
03 - In a saucepan over medium heat, melt 1 tablespoon butter. Stir in 1 tablespoon flour and cook for 1 minute. Slowly whisk in 1/2 cup milk, stirring constantly until thickened. Remove from heat. Add cheddar and Monterey Jack cheese to the sauce, stirring until melted and smooth. Season with ground black pepper. Add the cooked macaroni and stir to coat. Set aside.
04 - In a large bowl, combine all-purpose flour, yellow cornmeal, granulated sugar, baking powder, and salt.
05 - In a separate bowl, whisk together large eggs, 1 cup whole milk, and the melted and cooled unsalted butter. Pour the wet ingredients into the dry ingredients, mixing just until combined. Gently fold in the diced jalapeños.
06 - Spoon approximately 1 tablespoon of cornbread batter into the bottom of each muffin cup. Place a heaping tablespoon of the prepared mac and cheese filling on top of the batter. Cover the filling with another tablespoon of cornbread batter to fully enclose it.
07 - Bake for 18–20 minutes, or until the muffins are golden brown and a toothpick inserted into the cornbread portion comes out clean.
08 - Allow the muffins to cool for 5 minutes in the tin before transferring them to a wire rack. Serve warm.