Cheesy Mac and Cheese Muffins: Bite-Sized Comfort Food

Creamy mac and cheese is a beloved comfort food. If you want a more portable, portioned, and playful version, try these Mac and Cheese Muffins. They develop crisp, golden edges with a soft, cheesy center and work well for lunch, dinner, or snacks.

Mac and cheese muffins served with strawberries and broccoli.

Mac and cheese baked into muffin cups is a comforting twist on a classic. These muffin cups are rich and creamy inside with slightly crisp tops. They’re quick enough for weeknight dinners, portable for packed lunches, and kid-friendly for snacks. Serve them warm or cold — they’re versatile and easy to make.

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

These are the main ingredients for mac and cheese muffins:

Ingredients to make mac and cheese muffins.
  • Elbow macaroni — classic for mac and cheese; the shape holds sauce well.
  • Unsalted butter — forms the roux base and adds richness.
  • All-purpose flour — thickens the sauce so the muffins hold shape.
  • Whole milk — makes the sauce creamy (2% or unsweetened oat milk also work).
  • Cheddar cheese — sharp or mild, preferably freshly grated for best melting.
  • Cream cheese — adds extra creaminess and a touch of tang.
  • Seasonings — salt and paprika to taste.

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

Recipe Substitutions & Additions

  • Pasta: Small shapes like shells, rotini, or ditalini can replace elbow macaroni; keep to bite-sized pasta so the muffins hold together.
  • Butter: Substitute equal amounts of olive oil or avocado oil for a dairy-free option.
  • Flour: Use a 1:1 gluten-free flour or replace with 1 tablespoon cornstarch for a similar thickening effect.
  • Milk: Whole milk is ideal, but 2% or unsweetened plain oat milk work fine.
  • Cheese: Colby Jack, Monterey Jack, or mozzarella — or a blend — will work. Avoid pre-shredded cheese for smoother melt.
  • Cream cheese: Swap with Greek yogurt or sour cream in equal amounts for similar creaminess with extra tang.
  • Extras: Stir in cooked crumbled bacon, diced ham, or small steamed broccoli florets before baking for variation.

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 muffin mold.

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

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

Steps to make mac and cheese muffins.

Step 4: Gradually whisk in the milk until smooth. Simmer 2–3 minutes until the sauce begins to thicken.

Step 5: Reduce the heat to medium-low and add the cream cheese, whisking until it melts into the sauce. Remove from heat and stir in the shredded cheddar until smooth and creamy.

Step 6: Mix the cooked pasta into the cheese sauce until all noodles are coated.

Step 7: Divide the mac and cheese evenly among the muffin cups, pressing down so each cup is tightly packed. Sprinkle extra cheddar on top.

Step 8: Bake 20–25 minutes until the tops are lightly golden and set. Let rest for a few minutes, then carefully remove the muffins 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, place muffins in a freezer-safe container with parchment between layers and freeze up to 2 months; thaw in the refrigerator before reheating.

Mac and cheese muffins served with strawberries and broccoli.

Tips For Success

  • Grate your own cheese for smoother melting; pre-shredded cheese often contains anti-caking agents.
  • Don’t overcook the pasta — leave it slightly firm since it will bake again.
  • Silicone pans make removal easy. If using a metal tin, grease it well.
  • Press the mixture firmly into each cup so the muffins hold their shape after baking.
  • Let the muffins rest 5–10 minutes after baking to set before removing them from the pan.
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 rested longer before removal. Press the mixture firmly into each cup and allow the muffins to cool a few minutes before taking them out.

Can I serve these cold?

Yes — they’re tasty warm or cold, which makes them convenient for lunches. If you prefer them warm, pack in a thermos or reheat before serving.

Can I use different cheeses?

Absolutely. Colby Jack, Monterey Jack, mozzarella, or a blend all melt well. For the creamiest texture, avoid pre-shredded cheese if possible.

Other Lunch Recipes You’ll Love

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Broccoli Tots

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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 below — feedback is always appreciated!

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

Mac And Cheese Muffins

By: Lily Payen
A portable twist on classic mac and cheese — crispy on the outside and gooey in the middle, perfect for meals and on-the-go snacks.
Prep: 10 minutes mins
Cook: 25 minutes mins
Total: 35 minutes mins
Servings: 12 muffin cups
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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
US Customary – Metric

Instructions

  • Preheat the oven to 375°F (190°C) and grease a 12-cup muffin tin or use a silicone muffin mold.
  • Cook the elbow macaroni in boiling salted water until just al dente. Drain and set aside.
  • In a medium pan over medium heat, melt the butter. Whisk in the flour, salt, and paprika and cook about 1 minute to form a roux.
  • Slowly whisk in the milk until smooth. Simmer 2–3 minutes until the mixture thickens slightly.
  • Lower the heat and add the cream cheese, whisking until incorporated. Remove from heat and stir in the shredded cheddar until the sauce is smooth and creamy.
  • Add the cooked pasta to the cheese sauce and mix until fully coated.
  • Divide the mac and cheese into muffin cups, pressing down so they are tightly packed. Sprinkle extra cheddar on top.
  • Bake 20–25 minutes until tops are lightly golden and set. Let cool a few minutes, then gently remove the muffins from the tin.

Notes

  • Freshly grate cheese for the creamiest texture.
  • Keep pasta slightly firm to avoid mushy muffins.
  • Grease metal muffin pans well or use silicone for easy removal.
  • Pack the mixture firmly into each cup so muffins hold their shape.
  • Allow muffins to rest 5–10 minutes before removing for best results.

Nutrition

Calories: 203kcal, Carbohydrates: 17g, Protein: 8g, Fat: 11g

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