Macaroni and Cheese Muffins

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These single-portion macaroni and cheese muffins are a great healthy dinner for evenings on the go. They’re quick and easy to make.

These macaroni and cheese muffins are the perfect portable comfort food! Try them for dinner on a busy weeknight. Recipe from Real Food Real Deals.

During busy weeknights, it’s hard to get a healthy dinner on the table. Evening activities sometimes require dinner on the go, and these macaroni and cheese muffins are a lifesaver when I need to feed my kids a portable meal.

This recipe is for macaroni and cheese muffins with vegetables in the middle. It’s a meal all rolled up into one little muffin.

My husband thinks it’s a bit cruel to hide the vegetables like a prize in the middle (“Surprise! Broccoli and peas!”), but the children do enjoy them.

If you want to serve these muffins right out of the oven, I recommend lining the muffin pan with silicone muffin cups. This way, you can serve them in the silicone cups and they won’t fall apart.

Otherwise, cook these ahead of time and let them cool completely before removing them from the muffin pan. This will allow them to hold their shape. Transfer the muffins to the refrigerator or freezer, then reheat them when you’re ready to serve.

Try this easy homemade whole wheat calzone recipe for another healthy dinner on the go. And for dinner at home, try this delicious Instant Pot mac and cheese.

Macaroni and Cheese Muffins

These single-portion macaroni and cheese muffins are a great healthy dinner for evenings on the go. They're simple to make with an easy cheese sauce and a few green veggies.
Print Recipe
Prep Time:15 minutes
Cook Time:35 minutes
Total Time:50 minutes


  • 2 cups whole grain macaroni
  • 2 tbs butter
  • 2 tbs white whole wheat flour
  • 2 cups milk
  • 1 cup shredded cheddar cheese or more, to taste
  • Salt and pepper to taste
  • 1 cup uncooked broccoli florets
  • 1/2 cup frozen peas no need to defrost
  • 1/4 tsp paprika


  • Preheat the oven to 350 degrees and grease a 12-muffin pan or use paper liners.
  • Boil the macaroni according to the package instructions.
  • In a skillet, melt the butter and add the flour.  Whisk together over medium heat for a few minutes.
  • Gradually add the milk to the butter and flour.  Whisk constantly for about 5 minutes over medium heat until it begins to thicken.
  • Remove the skillet from the stove and stir in most of the cheese and all the macaroni.  Add salt and pepper if desired.
  • Fill each muffin cup with 2 tablespoons of the macaroni and cheese mixture.
  • Add a layer of broccoli or peas to each one.
  • On top of the vegetables, fill in each muffin tin with the remaining macaroni and cheese mixture and sprinkle paprika and the remaining cheese on top of each muffin.
  • Bake for 25-30 minutes, until muffins are just starting to turn brown on top.

Approximate Nutrition Info

Calories: 91kcal | Carbohydrates: 4g | Protein: 4g | Fat: 6g | Saturated Fat: 4g | Polyunsaturated Fat: 0.2g | Monounsaturated Fat: 1g | Trans Fat: 0.1g | Cholesterol: 19mg | Sodium: 95mg | Potassium: 110mg | Fiber: 1g | Sugar: 2g | Vitamin A: 333IU | Vitamin C: 9mg | Calcium: 123mg | Iron: 0.2mg
Servings: 12
Calories: 91kcal
Cost: $.23 per muffin

This recipe may contain affiliate links. A purchase or click through one of these links may result in a commission paid to us at no additional cost to you.

Macaroni and Cheese Muffins Price Breakdown

This recipe costs $2.81 to make, or $.23 each.  Macaroni and cheese muffins are a fun lunch or dinner for kids on the go.


  1. Pingback: A Breath of Fresh Air | Live Half Full
  2. this sounds yummy! can i use whole wheat flour instead of the white whole wheat flour? what difference would it make?

    1. Michele, I haven’t actually frozen these, but I think they’d hold up well. Let me know if you try it!

      1. I make these for my toddler and freeze. I bake them in a silicone cup, cool completely, remove the cup and put in a flat layer in a freezer bag. Make sure they are on a flat surface in the freezer. Once they are frozen they hold up great and thaw very well in the microwave. We love these!

      2. Thanks so much for letting me know, Niki. I’m glad your toddler enjoys these. Great tip about freezing them!

  3. I had been wanting to try these for a while. They were good but a little bland, even for me, and I do not like a lot of salt. My family ate them, but I am not sure how excited they would be for a repeat. I used unsalted butter, which could be the issue and did not salt the pasta water. To make them a little more kid interesting, I may do both of the above for next time and also try to add something else to sauce to give it more zing.

    1. Thanks for the feedback, Jeanne. The type of cheese you use will definitely impact the final product, so it’s always a good idea to taste and adjust seasonings as you go.

  4. I love this recipe! Any chance we could get the nutritional information? I try to keep an eye on fiber, fat, and protein with my busy family! Thanks!

    1. Sorry, I don’t do nutritional breakdowns. I believe there are tools online that will do this for you.

  5. I have also made corn dog muffins, they were good, but my kids aren’t big on hot dogs. My nephew loved them though. Possibly even kabobs to open up a bigger selection of foods! As long as your kids won’t poke an eye out with the stick or something of course!

  6. I cook meatloaf in muffin pans and my kids love it! We eat it at home so I top them with mashed potatoes so it looks like a cupcake, anything that resembles a cupcake is a win in my house! But just the meatloaf might work good for on the go asthe ketchup is mixed in and it has carrots and onions. You can also do eggs and sausage in muffin pans, my picky one loves eggs so we have them for dinner often! Or we make pizza puffs, I have toddlers so anything that can be eaten on the go we do a lot even at home.

    1. Great ideas, Brailey! Thank you. I will definitely try the mini-meatloaves. My daughter will love them.

  7. Wow, some great ideas!! Can you tell me which brand of whole wheat macaroni you like? I have not found a brand of macaroni we like. I love trader joes ww pasta, but they don’t carry macaroni.

    1. I actually don’t love any whole wheat macaroni, but I find that everyone in my family will tolerate whole wheat pasta as long as it’s covered with cheese! Have you tried the Hodgson Mill version?

  8. Mac & Cheese Muffins…what a fab idea!
    With two swim practices & five baseball games or practices each week, I’ve been struggling with suppers this spring.
    We’ve been making a lot of yogurt parfaits – greek yogurt, fruit, granola or grape nuts in insulated plastic drinking cups (minus the straw).
    Love the idea of upside down Shepard’s Pie, which got me thinking about searching for or experimenting with a taco/tamale muffin with corn muffin mix, taco filling & cheese.
    Dinner on the Dash!

    1. Sounds like you have it worse than me, Lollie. I love the corn muffin with taco filling idea, and I’m sure my children will too. Thanks!

  9. Those look yummy! We like fun little things like that so we’d probably love them. Putting on my thinking cap…mini/muffin tin meatloaves? Something in an egg roll wrapper? Anything inside a wrap. Baked Ravioli’s with a tiny cup of marinara for dipping?

    1. Wow, you’re good! Those are all great ideas. I’m planning to use your grated potato trick to line muffins at some point. Maybe an upside down shepherd’s pie with grated potatoes (with an egg binder) on the bottom and meat and veggies inside.

    1. It’s worth a try! I would suggest using paper cupcake liners because they do fall apart a bit.

  10. I think anything that can be prepared in muffin tins would be great! Cooked short-grain rice might work, too. You can smash it down, put a layer of shredded meat and veggies in between and put more rice on the top. In Hawaii you would find musubi, a rice ball (or triangle or rectangle) with filling inside or on the top wrapped with nori. 🙂

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