Easy Mac and Cheese Muffins with Crispy Onions

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These Mac and Cheese Muffins are easy to stack and store in the fridge and are a delicious way to use your leftover parmesan rinds. The parmesan rinds help thicken the cheesy mixture and impart a beautiful parmesan flavor. You can discard the rinds before you portion out the Mac and Cheese muffins or save them for making broth.

Makes 12 muffins

Easy Mac and Cheese Muffins with Crispy Onions



  • 3/4 lb. elbow macaroni pasta
  • 2 cups sharp cheddar cheese, grated
  • 1 cup swiss cheese, grated
  • ¼ cup Imperfect Foods Unsalted Butter, cut into cubes
  • ¼ cup all-purpose flour
  • 2 cups whole milk
  • 1 or 2 leftovers parmesan rinds
  • 4 cloves garlic, minced
  • Salt and pepper to taste


  • 1 cups panko bread crumbs 
  • 1 cup Imperfect Foods Crispy Onion pieces, pulsed to a crumble
  • ½ teaspoon salt
  • Chopped chives or scallions, for garnish  

Optional Materials

  • Cupcake liners


  1. Preheat oven to 400℉. Grease a 12-count muffin tin with cooking spray or butter or use cupcake liners.
  2. In a medium bowl, mix together bread crumbs, Imperfect Foods Crispy Onion pieces, and salt. Set aside.
  3. Cook pasta according to package directions. Drain and set aside.
  4. In a medium saucepan, melt butter over medium heat. Add flour and whisk until combined.
  5. Add minced garlic and stir. Add your parmesan rinds and then the milk, gradually stirring until there are no lumps of flour. Still whisking, increase heat to medium and bring to a light simmer. The mixture should be slightly thickened.
  6. Gradually add the shredded cheese and stir until melted and incorporated. Stir in cooked pasta. After the cheddar and swiss are incorporated, remove the parmesan rinds and discard (or rinse off and save for making broth).
  7. Portion the mac and cheese evenly into the muffin cups. Press down with the back of a spoon to pack the mixture into the cups. If not packed, they will have trouble holding their shape after baking. 
  8. Sprinkle each of the cups with the bread crumb mixture.
  9. Bake for 15 minutes. Remove and let cool for at least 10 minutes, then carefully run a butter knife around the edges to loosen. Remove the mac and cheese cups from the pan and garnish with chives or scallions. 

Recipe Notes and Variations

  • If you’re making these Mac and Cheese Muffins ahead of time, you can prep up to step 7 a day before you plan to eat them. Add the bread crumb topping and bake when you’re ready to eat!
  • We chose sharp cheddar and swiss cheese for their sharpness and nostalgic flavor, but if you prefer a more melty mac, you can swap out the swiss for mozzarella or gruyere.

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