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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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.

  25. I have made this recipe many times and every time it comes out grainy or chalky. II’ve tried longer roux cooking, warmer milk, cooler cream sauce before adding the cheese but to no avail its always grainy and it makes it not ao great. Does anyone else experience this and if so how do I correct it? Any tips would be great! Thanks!

  26. 5 stars
    Made this for dinner tonight with monterey cheese, peas, and bacon. It came out so good! I’m sure it will be even better with sharp cheddar next time!

  27. 5 stars
    This mac-n-cheese is awesome!!! Tonight was our first try. The whole family loved it! I added ground bison, broccoli and garlic powder. I used 1 lb of macaroni and it turned out the right consistency for us. We are now all plotting the variations we will make in the future, with peas, tuna, chili powder, and so on! I read through the previous comments – make sure you are following the steps exactly and use a good whisk when making your roux.

  28. 5 stars
    I was looking for something super quick and easy for dinner. Made this tonight. It was perfect! Added steamed veggies on the side and it was awesome. Thank you!

  29. 4 stars
    Have made this twice now. Of course the kids are having a hard time giving up the ‘other’ stuff, but they have taken to this much better than I expected. My husband and I really like it as well. As a family we are moving over to real foods/lower carbs (son recently diagnosed pre-diabetic) and are trying several of your recipes. Thanks for all that you do!
    Gave it 4 stars as “kid’s rating.” Mom would give it 5.

  30. Boiling noodles to make this RIGHT NOW!! I usually do a baked mac n cheese with alot more steps and it’s getting annoying.. lol. This looks super simple.

    1. Oh and my other one calls for temping in an egg, which is not easy and is very tiring. After doing all that I don’t even want to eat it anymore.. lol. This one is going well :)

    1. Assistant to 100 Days (Amy)

      Hello. It is pretty “sauce-y” as is. I guess it would depend on if you plan to add anything else to the recipe. You could always toast some cheese that you sprinkle on top toward the end of your baking time. ~Amy

    2. I didn’t make it into a casserole, but I did make it and put it into the crockpot – I have a newborn + toddler and needed to make it in the afternoon during naps. I doubled the recipe and used 3 cups of pasta (12 oz) and it could’ve used more sauce. I ended up pouring more milk into it before serving. I think if you were to make it a casserole you’d want to increase the sauce, too. Not sure how much though. If you double the pasta but triple the sauce, it may be too saucey…?

  31. Does anyone have a favorite brand of whole grain pasta to try? I’m drying to try this but last time I used whole grain pasta my kids hated it, and I have to admit I did too :-) Thinking I just got a bad brand. Thanks for any suggestions!

    1. We buy, on Amazon in bulk, “Hodgon Mill” Organic Whole Wheat Penne, “with milled flax seed.” It’s the ONLY pasta my kids will eat. They won’t even touch white pasta, though I still crave it now and again… Penne works fine in this recipe. It also is our kids favorite with spaghetti sauce.

  32. This was delicious! I can never get my daughter to eat homemade mac & cheese. She is very picky about color. (IMO, mac and cheese should NOT be orange, but her Dad likes to make the blue box for her.) She shredded the cheese while I did the roux, we added extra cheddar. She said, “You know Mom, I actually LIKE this!” The rest of us gobbled up an entire pound of it. I meant to have leftovers to freeze for lunches. Did not happen-every last cheesy noodle was eaten. Thanks for sharing recipes that keep us healthy and happy!

  33. Very Delicious! Whisk your flour into your cold milk and let it sit while you cook your noodles. Melt the butter, reduce to low and add your milk/flour, whisk until thickened, melt in cheese add noodles. Not grainy this way! I added half muenster (which is very creamy) and half cheddar, yum!

  34. Delicious!!! This was also very easy to prepare. I followed the other comments and made sure the ingredients were all room temperature. It turned out nice and creamy and very delicious! THANKS!!!

  35. 5 stars
    This mac & cheese is delicious! We doubled the recipe for six of us, used half mild cheddar and half monterey jack cheeses, and added frozen peas…my husband and four kids LOVED it! Since I always have to put a veggie on the side, we roasted butternut squash and had that, too. The combo of mac and cheese and squash sounds weird but it worked for us. :) Thank you for another awesome recipe!

  36. Made this tonight for the first time. I threw in frozen peas and both me and my 2 year old gobbled it up. It was delicious and not grainy at all. I used King Arthur WW flour and sharp Vermont white cheddar. Next time I’ll use less milk than 1 cup, as there was a little too much liquid.

  37. This was very easy. It didn’t have a very “cheesy” taste though, maybe because I used a medium cheddar. Next time I’ll try a mix of cheeses.

  38. 5 stars
    I cannot believe I just made Mac and cheese from scratch! It was delicious and my toddler gobbled it up! Though it was a tiny bit gritty I neglected to let my dairy ingredients get to room temperature.

  39. 5 stars
    This was delicious! I have a picky toddler and he gobbled this up. What are you recommendations for re-heating this for leftovers?

  40. Made this for dinner tonight. It was well received by all. We will definitely have again. Next time I will use sharp cheddar instead of mild cheddar. We give this recipe 4 stars.