Whole Wheat Macaroni and Cheese

24 Reviews / 4.8 Average
This Whole-Wheat Macaroni and Cheese recipe truly doesn’t take much more time than it would to make the highly processed macaroni out of a blue box. Don’t expect the same flavor as the factory made stuff though because it actually tastes SOOO much better.
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Whole wheat mac and cheese roux recipe with breadcrumbs in a small bowl

Whole Wheat Macaroni and Cheese Recipe

This recipe uses whole wheat macaroni and flour for a better-for-you alternative to processed boxed mac and cheese. Enjoy the classic comfort food without having to worry about the laundry list of ingredients in store bought mac. And, it’s totally freezer friendly! 

How to Make Mac and Cheese With Roux

The thing is, you barely take as much time to cook this homemade whole wheat mac and cheese as the box stuff! Using butter and whole-wheat flour, you whisk together the flour once the butter has completely melted. Once it’s darkened but not burnt, lower the heat and add the milk! 

It’s as easy as that, and you end up with a more flavorful and nutritious meal. The recipe below details these steps as well as all of the ingredients you need to make whole wheat macaroni and cheese!

Toppings for Homemade Macaroni and Cheese

Want to give this recipe a little more character of your own? There’s a plethora of ingredients you can add, here’s a few you might like to try:

  • More grated cheese! 
  • Whole wheat breadcrumbs 
  • Sliced green onion
  • Parmesan cheese 
  • Butter crackers 
  • A dash of paprika

How to Freeze Homemade Mac and Cheese

First, let the whole wheat macaroni and cheese cool completely. Next, seal it in a freezer container or airtight bag to prevent it from getting freezer burnt. It can stay fresh in the freezer for up to 3 months, after that give this recipe another go! 

And of course, this recipe is also much better for you with only a few simple ingredients including whole-grain noodles. So go ahead and do the right thing by making the switch for your family…it’s better late than never!

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217 thoughts on “Whole Wheat Macaroni and Cheese”

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Recipe Rating




  1. This is the best whole wheat macaroni and cheese recipe I ever made. It’s quick, easy, and so delicious! My family loves it and it’s the only macaroni and cheese we eat. Thanks for the recipe,

  2. Is this freezer friendly? With the new report on phthlates in boxed mac and cheese, string and pre-shredded cheese I need a quick, easy, and healthy mac and cheese that won’t take 10+ minutes to fix. Hoping I can fix a big recipe of this and freeze some for later?

    Thank you!

    1. Amy Taylor (comment moderator)

      Hi. I have frozen this successfully but there was a bit of separation when heating it back up. I mixed it back up pretty easily.

  3. 5 stars
    I made this for my daughter’s lunch today and with the first bite, she declared it delicious. She continued to rave about the food as she ate three bowls. I had been intimidated by homemade mac and cheese but it was super easy to make. I used half and half, as I did not have any unflavored milk, and it worked great. The sauce thickened quickly. Will be making this regularly.

  4. Hi, I want to make this for Thanksgiving but wondering if you can at least do part of it in advance? Would it be best to put it together in morning, refrigerate and then bake later in oven or do the whole recipe and then just reheat later?

      1. No problem! I actually got this recipe confused with the macaroni casserole recipe anyway from the cookbook. I put it all together and did end up refrigerating a few hours then added a few splashes of milk and baked. It was great!!

  5. My whole wheat flour is 2 years old. Is it dangerous to use in anything or just not ideal for a sensitive type of recipe? Would it be safe in this recipe?

    1. Amy Taylor (comment moderator)

      I would buy new flour. It might be okay if it was frozen but otherwise is likely rancid and would not taste great.