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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! Be sure to also try these Mac and Cheese Bites!
Whole-Wheat Macaroni and Cheese
Ingredients
- 1 cups whole-wheat macaroni ((boiled according to package directions))
- 2 tablespoons butter
- 2 tablespoons whole-wheat flour
- 1 cup milk
- 1 cup cheese (grated (you can use any type of cheese…we usually use sharp white cheddar or a mix of different cheeses works well too))
- salt (to taste)
- pepper (to taste)
- parmesan cheese (grated (optional topping))
Instructions
- Melt the butter in a sauté pan over medium heat.
- Whisk in the flour and keep whisking for about 1 - 2 minutes until the roux (which is equal parts flour and butter or oil) starts to darken, but does not burn.
- Turn the heat down to low and quickly whisk in the milk. Turn the heat back up to medium and keep whisking until the mixture starts to thicken and all lumps of flour are dissolved.
- Stir in the grated cheese and once it melts mix in the cooked noodles. Season with salt and pepper.
Serve immediately and enjoy!
Kim says
I am a bit confused about the amount of pasta this calls for. Can you clarify with the weight of pasta? Whole wheat elbow macaroni isn’t sold at my store and different shaped pasta will measure differently.
Elaine Drumm says
Can this be frozen ? Thinking healthier alternatives for my Granddaughter who eats Kraft microwaved Mac and Cheese
100 Days Admin says
Simple answer, yes, you can freeze it after you make it and let it get to room temperature, however, some people mention it separating when they reheat it. - Nicole
Stefanie says
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,
100 Days Admin says
So glad to hear everyone loves it. - Nicole
Sally Cully says
Why is there no nutritional info on your recipes?
Amy Taylor (comment moderator) says
Hi. This post will help you understand our philosophy on not providing nutrition details: https://www.100daysofrealfood.com/healthy-eating-defined/.
Holly says
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!
Amy Taylor (comment moderator) says
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.
Kim says
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.
Rebecca says
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?
Amy Taylor (comment moderator) says
Sorry that I'm late getting to this. How did it go?
Rebecca says
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!!
Jamie says
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?
Amy Taylor (comment moderator) says
I would buy new flour. It might be okay if it was frozen but otherwise is likely rancid and would not taste great.
LeeAnn says
A couple dashes of tabasco sauce is always nice!
Jessica says
Could I substitute the milk for Almond milk in this recipe? We don't normally cook with or drink milk. Thank you!
Amy Taylor (comment moderator) says
Hi there. Other readers have and I use almond milk in most of the recipes which call for milk.
Danielle says
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.
Katieliz says
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!
Joshua M says
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!
Katie says
This was delish!!! Thanks! No more boxes for us!
Sarah says
Would this be freezable to make for the week
Amy Taylor (comment moderator) says
Hi Sarah. Sure, you can freeze it!
Kaleigh says
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.
Kristi says
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!
shawn says
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.
Dolores says
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.
Stacey says
This was so easy and my 2 year old devoured it. I don't know why we haven't tried it sooner. Thanks, Lisa!
Amanda says
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.
Becky says
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!
Morgan says
Can you make this in ahead of time and then put in oven later on that evening?
Amy Taylor (comment moderator) says
Hi Morgan. You can. I've done it with some extra bread crumbs and graded cheese on top. ;) Enjoy.
Amanda says
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.
Amy Taylor (comment moderator) says
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.
Jacque says
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.
Tabby says
My sensory little one ate it up!
Marlana says
Delicious! I followed the recipe just as written and we all loved the results. This is a keeper. Thanks!
Shelley says
Looking for high protein recipes...i would assume this would be high in protien???
Amy Taylor (comment moderator) says
Hi Shelley. You can plug the ingredients into an online tool like My Fitness Pal and it will give you the nutrition breakdown.
Jen says
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!
Melissa says
Can you use coconut or almond milk?
Amy Taylor (comment moderator) says
Hi Melissa. You can. :)
Jillian Keller says
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. :)
Sarah says
Really?
Brooke M says
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!
Jen says
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!
Jennifer Sacco says
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!
David says
I tried this recipe last night and my kids loved it!
Ashley Haugh says
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.
Surrae says
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!
Clarissa says
Endless praising from all sides of the table every time I make this dish.
Kris says
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!
Quianna says
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!
Danielle says
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.