Cook the macaroni according to package instructions. Drain and set aside.
In a skillet, cook the bacon until crispy. Remove and set aside, leaving the bacon grease in the skillet.
Add the chopped jalapeños to the skillet and sauté until soft. Remove and set aside.
In a large pot, melt the butter over medium heat. Stir in the flour and cook for 1-2 minutes.
Gradually whisk in the milk, stirring constantly until the mixture thickens.
Add the shredded cheddar cheese, salt, and pepper. Stir until the cheese is melted and the sauce is smooth.
Stir in the cooked macaroni, bacon, and jalapeños. Mix well.
Transfer the mixture to a baking dish and bake at 350°F (175°C) for 15-20 minutes, until bubbly and golden on top.