Cheesy Mac and Cheese Muffins: Savory Bite-Sized Comfort Food

Creamy mac and cheese is timeless comfort food. If you want something a little more portable and portioned, these Mac and Cheese Muffins are a delicious twist. They have crispy edges and a gooey, cheesy center—perfect for lunch, dinner, or snacks.

Mac and cheese muffins served with strawberries and broccoli.

Baking mac and cheese into golden muffin cups makes a familiar favorite feel new and fun. These muffins are rich and creamy, yet easy to make—great for weeknight dinners, school lunches, or make-ahead snacks. Serve them warm at the table or pack them cold for lunch boxes.

Table of Contents

  • What You’ll Need
  • Recipe Substitutions & Additions
  • Step-by-step Instructions
  • Storage Instructions
  • Tips For Success
  • Recipe FAQs
  • Other Lunch Recipes You’ll Love
  • Mac And Cheese Muffins Recipe

What You’ll Need

Ingredients for the mac and cheese muffins:

Ingredients to make mac and cheese muffins.
  • Elbow macaroni – holds sauce well and is classic for mac and cheese.
  • Butter – builds the roux and adds richness.
  • All-purpose flour – thickens the cheese sauce so muffins hold together.
  • Whole milk – creates a creamy base; 2% or unsweetened plain oat milk will also work.
  • Cheddar cheese – sharp or mild; freshly grated melts best.
  • Cream cheese – adds extra creaminess and a touch of tang.
  • Seasonings – salt and paprika to taste.

See the recipe card below for exact ingredient amounts and full recipe details.

Recipe Substitutions & Additions

  • Pasta: Any small, bite-sized pasta (shells, rotini, ditalini) works well.
  • Butter: Swap with olive or avocado oil for a dairy-free option.
  • Flour: Use a 1:1 gluten-free flour or 1 tbsp cornstarch instead of 2 tbsp flour for thickening.
  • Milk: Whole milk, 2%, or unsweetened plain oat milk are all fine choices.
  • Cheese: Colby Jack, Monterey Jack, or mozzarella are good alternatives; avoid pre-shredded if possible.
  • Cream cheese: Greek yogurt or sour cream can be used in equal amounts for a similar texture with more tang.
  • Extras: Stir in cooked bacon, diced ham, or steamed broccoli before baking for added flavor and variety.

Step-by-step Instructions

Steps to make mac and cheese muffins.

STEP 1: Preheat the oven to 375°F (190°C) and grease a 12-cup muffin tin (or use a silicone mold).

STEP 2: Cook the elbow macaroni in boiling salted water until just al dente. Drain and set aside.

STEP 3: In a medium pan over medium heat, melt the butter. Whisk in the flour, salt, and paprika for about 1 minute to form a roux.

Steps to make mac and cheese muffins.

STEP 4: Slowly whisk in the milk until smooth. Simmer 2–3 minutes until the mixture begins to thicken.

STEP 5: Reduce heat to medium-low and whisk in the cream cheese until fully incorporated. Remove from heat and stir in the shredded cheddar until the sauce is smooth and creamy.

STEP 6: Add the cooked pasta to the cheese sauce and stir until all noodles are evenly coated.

STEP 7: Divide the mac and cheese among the muffin cups, pressing down gently so they are tightly packed. Top each cup with extra cheddar.

STEP 8: Bake 20–25 minutes until the tops are lightly golden and set. Let the muffins cool a few minutes, then remove them gently from the tin.

Storage Instructions

Store cooled muffins in an airtight container in the refrigerator for 3–4 days. Reheat in the oven, air fryer, or microwave until warmed through. To freeze, arrange muffins in a freezer-safe container with parchment between layers and freeze up to 2 months.

Mac and cheese muffins served with strawberries and broccoli.

Tips For Success

  • Grate your own cheese for better melting—pre-shredded cheese often contains anti-caking agents that affect texture.
  • Cook pasta just to al dente since it will bake again.
  • Use silicone pans for easy removal, or grease metal pans well to prevent sticking.
  • Press the mixture firmly into each cup so the muffins hold their shape after baking.
  • Let the muffins rest for 5–10 minutes after baking to set, which makes removal easier.
Mac and cheese muffins served with strawberries and broccoli.

Recipe FAQs

Why aren’t my mac and cheese muffins holding their shape?

Usually they need to be packed more tightly or cooled slightly before removing. Press the mixture firmly into each cup and let them rest a few minutes after baking.

Can I serve these cold?

Yes. They’re tasty warm or cold, which makes them a convenient option for lunches.

Can I use different cheeses?

Yes. Colby Jack, Monterey Jack, or mozzarella work well. For best results, avoid pre-shredded cheese.

Other Lunch Recipes You’ll Love

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Mini Chicken Tacos

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Broccoli Tots

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Cheeseburger Bombs

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Chicken Bacon Ranch Quesadillas

If you tried these Mac and Cheese Muffins, please leave a star rating and share how they turned out in the comments—I love hearing from you!

Mac and cheese muffins served with strawberries and broccoli.
5 from 2 votes

Mac And Cheese Muffins

By: Lily Payen
These mac and cheese muffins are a portable, portioned take on classic creamy mac and cheese—crispy on the outside and melty inside.
Prep: 10 mins
Cook: 25 mins
Total: 35 mins
Servings: 12 muffin cups

Ingredients 

  • 8 oz elbow macaroni, about 2 cups dry noodles
  • 2 tbsp unsalted butter
  • 2 tbsp all purpose flour
  • 1 ½ cups whole milk
  • ¼ tsp salt
  • ¼ tsp paprika
  • ¼ cup cream cheese
  • 2 cups shredded cheddar cheese, plus more to sprinkle on top

Instructions 

  • Preheat oven to 375°F (190°C) and grease a 12-cup muffin tin (or use a silicone mold).
  • Cook elbow macaroni in salted boiling water until just al dente. Drain and set aside.
  • Melt butter in a medium pan over medium heat. Whisk in flour, salt, and paprika for about 1 minute to form a roux.
  • Slowly whisk in milk until smooth. Simmer 2–3 minutes until the mixture thickens.
  • Lower heat to medium-low and add cream cheese, whisking until incorporated. Turn off heat and stir in shredded cheddar until the sauce is smooth.
  • Add cooked pasta to the cheese sauce and stir until fully coated.
  • Divide mac and cheese among muffin cups, pressing down firmly. Sprinkle extra cheddar on top.
  • Bake 20–25 minutes until tops are lightly golden and set. Cool a few minutes before removing from the tin.

Notes

  • Grate your own cheese for the best melting and texture.
  • Don’t overcook the pasta—leave a slight bite.
  • Grease metal pans well or use silicone pans for easy removal.
  • Press the mixture firmly into cups so muffins keep their shape.
  • Let muffins rest 5–10 minutes to set before removing.

Nutrition

Calories: 203kcal, Carbohydrates: 17g, Protein: 8g

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