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Mac and Cheese Muffins

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5 from 3 votes

These Mac and Cheese Muffins are crispy on the outside, creamy and cheesy on the inside, and downright addictive. Perfectly portioned for easy serving, they’re a fun and impressive twist on the classic Thanksgiving side that’s guaranteed to steal the spotlight.

mac and cheese muffins topped with breadcrumbs on speckled plate.

Put these Cheesy Muffins on your menu

This Mac and Cheese Muffin recipe is going to knock your socks off. I tested this recipe 5 times before landing on the perfect recipe and that’s because not all cheese is created equal. 

They went from pretty bland to too creamy to needs more sharp cheddar to not enough salt to *ah, ha* perfection. Because let’s be honest, if you’re making mac and cheese at Thanksgiving, it NEEDS to be show stopping. 

They’re a fun addition to the holiday spread because they’re unique, but still hit home on as a classic dish that is expected on the table. I also love these muffins because they’re perfectly portioned. Easy to grab one (or two or three;)), or even serve them as a finger food appetizer that even picky eaters will love!

And if you’re looking for another macaroni and cheese recipe, also try my Gouda Baked Mac and Cheese or this Chicken Ranch Mac and Cheese for something even heartier. 

Recipe Ingredients

ingredients for mac and cheese muffins in individual bowls.
  • Noodles – Elbow noodles, like classic macaroni. They also hold their shape well in the muffin form.
  • Roux – Made from butter and all purpose flour.
  • Spices – Garlic, oregano and black pepper.
  • Milk – 2% or whole milk to form the sauce.
  • Cheese NOT ALL CHEESE IS CREATED EQUAL. You need to have 3 strongly flavorful cheeses (like sharp cheddar, aged gouda, flavored sharp cheddar / parmesan) instead of softer cheeses like havarti, American, or Colby jack. I tested with these milder cheese and the result was very bland.
  • Egg – To give the muffins structure.
  • Cottage Cheese – For an extra creamy sauce.
  • Breadcrumb topping – Made with breadcrumbs, ritz crackers, garlic, oregano, salt, pepper and olive oil.

See the recipe card below for a full list of ingredients and measurements.

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Substitutions and Variations

  • Prefer a big ‘ol scoop of macaroni instead? Just bake this mac and cheese in an 8×8 / 9×9 pan instead!I wouldn’t recommend 9×13 as its too shallow and the result will be too dry.
  • Try adding some mix-ins like sauteed veggies like onions, broccoli or cauliflower. Consider adding a protein like shredded chicken, bacon or ground sausage. 

How to Make This Recipe

elbow noodles in water cooking in black sauce pot.

1. Heat a sauce pot with water and bring to a boil. When the water is boiling, add the elbow macaroni noodles and cook them 1 minute less than the box says to. Strain the noodles and put them into a large mixing bowl. Set aside.

creamy mac and cheese muffin sauce in large sauce pot.

2. In the same sauce pot, heat to medium low heat. Add the butter and flour. Melt butter and whisk so a roux forms. Add the seasonings, continue to stir. Once a paste forms, pour in the milk and continue whisking.

3. When the roux has thickened, add all of the shredded cheese. Whisk until it’s dissolved. Remove from heat.

ingredients for mac and cheese muffin in glass mixing bowl.

4. Preheat the oven to 350F. Pour the cheese into the large bowl with the cooked noodles, along with the egg and cottage cheese. **we do not want the egg to cook with the hot cheese mixture. Cool it slightly before pouring.

mac and cheese muffin batter in gray muffin tin.

5. Mix all together until creamy mac and cheese has formed. Spray a muffin tray with nonstick cooking spray **note: if your muffin pan is not non-stick, I would use muffin liners or silicone cups. I’ve only tested with my slick Caraway muffin pan and every time they’ve come out NO issues. You’ll know what’s best with your muffin pan. Use a cookie scoop to distribute mac and cheese into each.

toasted bread crumbs in black skillet with wooden spoon in pan.

6. Heat a small skillet to medium-low heat. Add all of the breadcrumb topping into the skillet and toss together until lightly toasted. Watch it carefully as it can burn quickly.

mac and cheese muffins in gray muffin tin topped with bread crumbs.

7. Use a spoon to scoop the toasted breadcrumbs onto each mac and cheese top. Bake for 18-22 minutes until the edges of each cup have formed and the bread crumbs are golden brown.

8. Allow to cool slightly before removing (its hot cheese, it needs a second to form)! Enjoy warm!!

PRO TIPS

  • We slightly under cook the noodles as we don’t want them to be soggy once they’re baked. 

Recipe FAQs

How do we store it? 

Store your leftover Macaroni and Cheese Cups in an airtight container for 3-4 days. Reheat in the microwave for 60-90 seconds until warm throughout.

Can I make these ahead of time?

Yes! You can bake them a day in advance and reheat in the oven at 350°F for about 10 minutes the next day to crisp them back up.

Do I need to use muffin liners?

Only if your muffin pan isn’t nonstick should you need muffin cups. Otherwise, just spray generously with cooking spray and they’ll pop right out.

How do I prevent the muffins from falling apart?

Let them cool for a few minutes after baking so the cheese sets — that helps them hold their shape when removed from the pan.

Serving suggestions

Make these muffins as a Thanksgiving side dish along with these Bacon Wrapped Apples and Parmesan Crusted Brussels. Or make the mac and cheese muffins on a cozy fall weekend with some Spicy Butternut Squash Soup

mac and cheese muffins topped with breadcrumbs on speckled plate.

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Homemade Trader Joe’s Butternut Squash Mac and Cheese

Chicken Ranch Mac and Cheese

Mac and Cheese Muffins

5 from 3 votes
Prep20 minutes
Cook20 minutes
Total40 minutes
Servings12
These Mac and Cheese Muffins are crispy on the outside, creamy and cheesy on the inside, and downright addictive. Perfectly portioned for easy serving, they’re a fun and impressive twist on the classic Thanksgiving side that’s guaranteed to steal the spotlight.
Save This Recipe form

Save This Recipe!

Enter your email below & we’ll send it straight to your inbox. Plus you’ll get great new recipes from us every week!

Equipment

  • sauce pan
  • Whisk
  • skillet
  • Measuring cups and spoons
  • Mixing Bowl
  • muffin pan
  • Cookie scoop

Ingredients

  • 1 ¼ cup uncooked elbow noodles
  • 3 tbsp butter, unsalted
  • 3 tbsp all purpose flour
  • 1/2 tsp garlic powder
  • 1/2 tsp oregano
  • 1/4 tsp black pepper
  • 1 cup Milk, 2% or whole
  • 1 cup sharp cheddar cheese, shredded
  • 1 cup white cheddar cheese, shredded
  • 1/4 cup parmesan
  • 1 egg
  • ½ cup cottage cheese, 4% whole milk fat

Bread Crumb Topping

  • 1 tsp olive oil
  • 1/2 cup panko breadcrumbs
  • 1/4 cup Ritz crackers, crushed
  • 1/2 tsp garlic powder
  • 1/2 tsp oregano
  • 1/4 tsp black pepper
  • pinch Salt

Instructions

  • Heat a sauce pot with water and bring to a boil. When the water is boiling, add the elbow macaroni noodles and cook them 1 minute less than the box says to. Strain the noodles and put them into a large mixing bowl. Set aside.
  • In the same sauce pot, heat to medium low heat. Add the butter and flour. Melt butter and whisk so a roux forms. Add the seasonings, continue to stir. Once a paste forms, pour in the milk and continue whisking.
    creamy mac and cheese muffin sauce in large sauce pot.
  • When the roux has thickened, add all of the shredded cheese. Whisk until it’s dissolved. Remove from heat.
  • Preheat the oven to 350F. Pour the cheese into the large bowl with the cooked noodles, along with the egg and cottage cheese. **we do not want the egg to cook with the hot cheese mixture. Cool it slightly before pouring.
    ingredients for mac and cheese muffin in glass mixing bowl.
  • Mix all together until creamy mac and cheese has formed. Spray a muffin tray with nonstick cooking spray and use a cookie scoop to distribute mac and cheese into each.
  • Heat a small skillet to medium-low heat. Add all of the breadcrumb topping into the skillet and toss together until lightly toasted. Watch it carefully as it can burn quickly.
    toasted bread crumbs in black skillet with wooden spoon in pan.
  • Use a spoon to scoop the toasted breadcrumbs onto each mac and cheese top. Bake for 18-22 minutes until the edges of each cup have formed and the bread crumbs are golden brown.
    mac and cheese muffins in gray muffin tin topped with bread crumbs.
  • Allow to cool slightly before removing (its hot cheese, it needs a second to form)! Enjoy warm!!

Nutrition

Serving: 1muffin | Calories: 204kcal | Carbohydrates: 15g | Protein: 10g | Fat: 12g | Saturated Fat: 6g | Monounsaturated Fat: 2g | Cholesterol: 48mg | Sodium: 262mg | Potassium: 69mg | Fiber: 1g | Sugar: 2g

Video

Notes

If your muffin pan is not non-stick, I would use muffin liners or silicone cups. I’ve only tested with my slick Caraway muffin pan and every time they’ve come out NO issues. You’ll know what’s best with your muffin pan. 
NOT ALL CHEESE IS CREATED EQUAL. You need to have 3 strongly flavorful cheeses (like sharp cheddar, aged gouda, flavored sharp cheddar / parmesan) instead of softer cheeses like havarti, American, or Colby jack. I tested with these milder cheese and the result was very bland.
Store in an airtight container for 3-4 days. Reheat in the microwave for 60-90 seconds until warm throughout.
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5 from 3 votes

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