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.

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

- 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.
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

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.

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.

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.

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.

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.

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
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.
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.
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.
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.

More Recipes You’ll Love
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Mac and Cheese Muffins
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.

- 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.

- 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.

- 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.

- Allow to cool slightly before removing (its hot cheese, it needs a second to form)! Enjoy warm!!
Nutrition
Video
Notes
Looking for this in MyFitnessPal?
If you’re using MyFitnessPal, search ‘A Paige Of Positivity’ and find Mac and Cheese Muffins calories and nutrition facts. Disclaimer: for most accurate macronutrients and caloric breakdown, it is recommended that you input each ingredient into your MyFitnessPal food diary.
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oh MY! handheld mac and cheese. say LESS. the bread crumb topping is irresistable.
ok we LOVED these!
Now this is comfort food, the breadcrumbs are a nice touch.