Preheat oven to 400 degrees F. Boil pasta according to package directions. Drain and set aside.
In the same pot, melt 4 tablespoons butter. Add diced onion and cook for 8 to 10 minutes, until onion is soft and translucent.Add diced jalapeno and cook another 1 to 2 minutes. Stir in ¼ cup flour and continue to stir for 2 minutes to cook flour. Add ½ teaspoon dried mustard and stir in milk. Bring to a simmer and cook until sauce starts to thicken, about 3 minutes.
Once sauce is thick, remove from heat and stir in shredded cheese, reserving ½ cup. Stir until cheese is melted, then season with salt and pepper. Fold in macaroni until well combined.
Pour mixture into an 8-inch square baking dish. Sprinkle top with the reserved shredded cheese. Melt the remaining 4 tablespoons butter and stir in 1 cup breadcrumbs. Evenly spread breadcrumb mix on top of dish to cover.
Bake for 25 minutes, until cheese starts to bubble and breadcrumb topping is browned. Let rest for 5 to 10 minutes and serve.