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.

  6. Could I substitute the milk for Almond milk in this recipe? We don’t normally cook with or drink milk. Thank you!

    1. Amy Taylor (comment moderator)

      Hi there. Other readers have and I use almond milk in most of the recipes which call for milk.

  7. 4 stars
    Very yummy and quick. Made it tonight for a last minute dinner. I sauteed a little onion and green pepper and chopped up a left over bratwurst and added it.

  8. 5 stars
    This is fantastic!! Last night at dinner, my five YO couldn’t express enough appreciation for it :) Even tried to convince his little brother to try it. I will definitely be making this again and again. Easy and delicious. Reheated fine today, just a little oil separation, but still creamy. Thanks, Lisa!

  9. Definitely going to have to attempt this. Though I did have a recipe I’d tried before which said to boil the noodles in the milk(and it works somehow I’m still a little confused on that matter ha ha), and then you add the cheese and such afterwards(and a tablespoon of flour might help it because it does end up a little runny sometimes). But I ended up with it using half cheddar and half parm, it’s a amazing combo!

  10. 5 stars
    So good! It really is quick and easy to make and I’ll never use the processed stuff out of the box again! My husband loves it and can’t contain his excitement when I tell him that we’ll be having it for dinner. I actually asked him if he would rather have this macaroni and cheese recipe for dinner or steak (his favorite), and he couldn’t choose, which speaks volumes about how good this recipe is.

  11. I am not sure what I did wrong here. I followed the directions to a T but mine came out so runny and the cheese/milk mixture never quite incorporated. I was extremely careful not to cook over the specified temp as I know the cheese can separate and become stringy. The sauce also didn’t “grab” onto the noodles as I would prefer. The flavor was fine but the texture was a miss. Any advice for the next time is greatly appreciated!

    1. Hi Kristi, Sorry that it didn’t turn out right for you. It is supposed to thicken. You may need to cook the milk more before you add the cheese.

      1. Hi Kristi, It sounds like you may have missed the flour or either had too little flour or too much milk. Once you cook the butter and flour and add the milk it will thicken as it cooks. Though the recipe doesn’t specify how long it needs to cook it is important to bring the milk and flour mixture to a boil while whisking constantly to prevent burning. It needs to boil lightly because this cooks and thickens the flour. I have had great success by letting it boil lightly for 2 minutes and then lowering the heat and cooking, whisking constantly, for another 5-10 minutes. Once it has cooked you can take it off the heat and stir in the cheese which will melt nicely without cooking it. Hope this helps.

  12. 3 stars
    Another one to add to the rotation. Super quick and easy to make. Follow the directions exactly – first time I made this I didn’t and it was a gooey mess. Not as good as Mom’s but definitely a repeat for it’s speed and quality as a side or main.

  13. we have only had the blue box a few times with the kids mainly during lent and when I was pregnant with morning sickness and it was the only thing I could keep down…so when my daughter asked for Mac and cheese it surprised me but I thought I will check out your recipe…I was delicious! and the kids loved! I used Colby Jack and and Parmesan for the cheese and it turned out great thanks for the recipe!

    1. Amy Taylor (comment moderator)

      Hi Morgan. You can. I’ve done it with some extra bread crumbs and graded cheese on top. ;) Enjoy.

  14. I’m curious about the consistency of this. I tried a recipe last week for an old fashioned mac and cheese and it came out very grainy. My kids liked it but I didn’t. My boyfriend has introduced me to unprocessed eating as that is how he and his family eat (and I’ll be expected to cook that way when I move in). I am trying to find recipes that I can start using now before I make the move so that I am already in the habit of cooking/shopping without all of the highly processed crap that is so easy to grab.

    1. Amy Taylor (comment moderator)

      Hi Amanda. Over heating the cheese added to the roux can make the proteins clump. That can lead to a grainy texture. Also, whole wheat noodles are also going to have a different texture than the white stuff you are likely used to. You could also try using a creamery type of cheese.

    2. I have tried tons of recipes for mac and cheese and my husband and I have never enjoyed the grainy texture that adding the whole wheat flour has given. I found a recipe recently that you cook the noodles in the whole milk and then once tender (longer than the box says) take off and stir in your butter and cheese= amazing consistency. (No flour needed) I won’t ever make it another way now. I do recommend adding salt and pepper as you boil the noodles.

    1. Amy Taylor (comment moderator)

      Hi Shelley. You can plug the ingredients into an online tool like My Fitness Pal and it will give you the nutrition breakdown.

  15. 5 stars
    I have a 15 month old who will eat practically anything. There are only a handful of things that she has expressed a distaste for, surprisingly, one of those things is boxed macaroni and cheese. I made this last night and she devoured it! I have learned so much about healthy cooking from your website! I love making guilt free wholesome meals for my family!

  16. One way to make this SUPER easy and avoid more than one pot is too cook the noodles on low in Organic Whole Millk until noodles are soft. Then you skip making the base for the sauce, just add your cheese when it’s done and stir. :)

  17. I’ve been making this for awhile and really like it- but it was SO thick that it didn’t quite satisfy my low-brow mac and cheese cravings, since the box brands often have a smooth, kind of runny, sauce. On a whim the other day, I made a doubled this recipe and cooked a full pound of noodles. I reserved about a cup and a half of pasta water before draining. I made the sauce as directed, then slowly stirred in the pasta water until the sauce reached a creamier, runnier consistency. Perfect!

  18. 5 stars
    Started 10 day challenge today and the kids were asking for Mac & cheese so I made this. Wow! What a hit. We all loved it!! This will absolutely be a go-to meal for us!

  19. 5 stars
    I actually made this recipe before I found your website and I will vouch for how absolutely delicious and satisfying it is… and I’m a die hard box mac and cheese fan… this is truly the first homemade mac and cheese I’ve ever liked! And I liked it as much if not more than my usual fav Kraft mac and cheese!!

    I love reading about your journey and how obtainable it really is!

  20. This was so good, and so quick to make. I shredded the cheese while waiting for the water to boil, and started the sauce when I put in the noodles. They were done at the same time. I did add garlic and onion powder too. Delicious. Oh, I doubled the sauce, and used a 1lb box of pasta, and it was the perfect consistency.

  21. 5 stars
    I made this last night. We are making the effort to switch over to a real food diet. This recipe was perfect and kept my Kraft Mac obsessed husband happy. I will be making more to freeze for his lunches!

  22. Hi! I just wanted to let you know that I have been using the first part (butter,flour,milk,cheese) to make a cheese sauce for when we have our taco/nacho night! Delicious! The kids love it! Thanks!

  23. Amy – I did use whole milk and full fat cheese. I know it happens before the cheese goes in because I have tasted the sauce before adding the cheese. I also tried warming the milk and cheese before adding it. I actually found a recipe for homemade velveeta which I used to use regularly for mac n cheese (gross I know!) If I cant figure out this one I’ll use my new homemade velveeta. Thanks!

  24. I just made this for my 1 year old for lunch and she ate an entire bowl! I used mozzarella and Gouda cheeses because that’s what I had on hand. Also, I chopped up some broccoli and cauliflower just to see if I could sneak in some extra veggies. We both loved it! Thanks for the great recipe.