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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!
Krissy says
I double this, and add tuna and peas for a nice, yummy meal. Family loves it!
Mehgan says
So here is what I did for this one. I used almond milk instead of dairy and a little more than 1 cup of grass fed mild cheddar cheese. I also added a teaspoon of garlic and onion as well as a pinch of salt. I also added a little parmesan.
While cooking the recipe, I did follow the directions except I forgot to cook the noodles before making the sauce. So I just kept the milk in with the roux on medium low and kept stirring. Yes my almond milk was boiling slightly, but my sauce did not turn out gritty. After 5 minutes of this my noodles were finally done so I added in my cheese, let it melt, then added in my noodles. So with almond milk at least, it seems fine to let it boil a little if you need to once you add it to the roux.
It turned out creamy and delicious. A much better version of white cheddar :) I can't believe I made home made mac n' cheese!
Jennifer says
I made it gluten free tonight with rice noodles and used the butter, super fine brown rice flour, Trader Joe's lite coconut milk and extra sharp cheddar. Yum. Can't wait for the leftovers.
Vivian says
Jennifer: Does the Trader Joe's light coconut milk contain carrageenan? That's a red algae that is a carcinogen, causes inflammation & intestinal abnormalities. I used to think it was seaweed, but why is it in coconut milk?
kathryn says
This was so easy and so delicious! Just made it for my daughter's lunch and I'm hoping she loves it as much as I do. She loves the frozen Amy's mac&cheese, but I've been searching for a healthy, homemade alternative. Thank you-love your site...so inspiring!
Sarah says
I find the best Mac and cheese is when I boil the noddles in just enough milk- then as cheese and spices. Holy moly it's good and thick and creamy!
Amy D. says
It tasted great, but I do agree with Katelyn's comment about it being gritty. I think I'll try a finer flour next time (like whole-wheat pastry flour, maybe) and let you know how it turns out.
(^_^)
Amy D. says
On a side note, it was not as gritty when I had the leftovers the next day because I added a little milk to get it creamy again in the microwave. Can't wait to try it again! (^_^)
Amy D. says
Made it with whole wheat pastry flour this past weekend. While slightly less gritty (I figured out I just need to add a bit more milk to combat that) it did not thicken the sauce nearly as much as the white whole wheat flour did. Switching back to that now. Can't wait until I have enough saved up for my own wheat grinder so I can make my own flour! (^_^)
Krystal says
Can you sub the milk door almond milk and utter for Ghee? If so, same measurements?
Krystal says
I mean sub the milk FOR almond milk and sub the butter for ghee?
Assistant to 100 Days (Jill) says
Hi Krystal. I have not tried it, but, you can give it a try. I'm not sure it will taste the same (I'm guessing it will be less creamy with the almond milk). Let us know how it turns out. Jill
Katelyn says
I've tried this before and while my 2 year old eats it fine, it just doesn't do it for me. I grew up on velveeta used for "homemade" mac and cheese (not the boxed stuff.) This always ends up just a bit gritty even when shredding my own block cheese. I may try different cheeses or without the roux.
Assistant to 100 Days (Jill) says
Hi Katelyn. Sorry you haven't enjoyed this recipe. Hope you have had some luck with changing it up a bit to suit your tastes. Thanks for the feedback. Jill
Becca says
This recipe is very similar to the mac & cheese I grew up on! Instead of a whole cup of milk, my mom used 1/2 c. milk and 1/2 plain yogurt. She also adds a dash of mustard (the wet kind). Both of these changes give it really good flavor! I just made it tonight. Mmmmm!
kathleen kiley says
So good...made this from the recipe and this time I used the suggestions Becca left.
Was so yummy. My yogurt broke a bit and was thin but I was patient and let it cook a bit more and it thickened up and was eaten by my son and by me!
Thanks
Carly says
Amazing how easy this was! And I kept putting it off thinking it'd be time consuming! Why use a box again!!??
Kim says
I just made this for my picky picky toddler. He's eating it! I even stirred in some pureed carrots too. We both enjoyed it for lunch. Thanks!
Sile says
I'm curious as to what brand of pasta you use? I saw in an earlier post that the wheat barilla wasn't really whole wheat, and it made me wonder what you use... I know you've made some pasta from scratch, but you don't do that for mac n cheese, do you? :)
Assistant to 100 Days (Jill) says
Hi Sile. I use the Bionaturae. You can find it here...https://www.100daysofrealfood.com/my-kitchen-essentials/#other. No, I do not make homemade pasta for mac n cheese! Jill
Kim says
Made this tonight and all 5 of us LOVED it! My daughter (9) ate all of hers and said it was the BEST mac n cheese she's ever had and before this week we've always made Kraft or Velveeta and did not eat Real Food at all. So HUGE compliment! My other kids are 5 and 3 and ate it just like they would have the boxed stuff. We steamed some broccoli with a little low sodium soy sauce for a side.
Danielle says
Ive been making a similar version for years. I can't even eat the boxed kind anymore. Mine uses one rounded tablespoon of butter and a little more cheese and noodles. I also add some puréed cauliflower for extra veggies. Love the blog! Was up half the night reading past ones lol!
Jessica Ali says
The first time I tried this,it was awful! I just couldn't figure it out. So then I reread the instructions and realized the first time I added the cheese in before the milk with the butter flour mixture could thicken. So i whisked and whisked and abut minute and a half later it started getting thick. I immediately added the cheese then turned off the heat, stirring until it all melted and then added the noodles. I undercooked my noodles though! GRRRR. But, the cheese sauce tasted amazing which was of course the most important thing. So for those of you who don't like it, try again. I sure am happy I did!!
Susan says
We made this for lunch this past weekend...we added grilled chicken and steamed broccoli. My husband said it was the best macoroni and cheese he has ever eaten! We devoured it! And it was pretty easy to make too!
Katie says
I have a really dumb question. Is 1 - 1 1/2 cups of dry pasta equal to 8 to 12 oz. measured? I made this last night with whole wheat shells and it was delicious, my duaghter loved and said she liked it better than "regular" mac and cheese, but I think I used too much pasta.
I made several other recipes off the blog and they have all been fantastic, thanks for helping us get healthier!
Assistant to 100 Days (Jill) says
Hi Katie. Well 16 oz is a pound, so, I'm thinking it's about 8 ozs, or 1/2 pound. I'm just guessing though, I'm not actually measuring it out. Glad you're enjoying the blog and recipes. Jill
Marie says
The box of pasta I used was a 12 oz box and it said it was 6 x 1/2 cup (dry) servings. So 3 cups.
Thing with using a "cups" measurement for the pasta is that I would think the different shapes/sizes would "pack" differently and therefore measure differently. For example, I would think a cup of macaroni would be more pasta than a cup of penne.
Sarae says
We recently ate all our blue box stuff and I vowed to replace foods with non processed as we go. This is the first recipe I tried and my girls (2&5) who are both VERY picky loved it. Its also much hardier and filling than the box stuff and I can get a few lunches out of one pot. I cant wait to try the rest of the yummy recipes on here =) My family and I are looking forward to a "real food" future. THANK YOU!!!!
Stacy says
I had the gritty problem once and I think I just didn't get the flour lumps out well enough. But last night I totally forgot the 2nd tbs of flour until I was stirring the cheese sauce and thinking "this sure looks thin!". It was too watery to use, so I took the chance and put the other tbs of flour in at that point. I did just a little at a time, whisking it constantly. It ended up being the best that I've made, soooo creamy, and I've made the recipe about 5 times. Not sure if it was just coincidence.
Sara says
Made this today and all three of my kids LOVED it!! The older two fought over helping me make it even! My 3 yr old asks for mac and cheese 4 out of 5 days a week and with this recipe, I won't mind making it as much! Quick and easy but much better than that ol' blue box :) Thank you!!
Ann says
Hi Lisa,
First off I LOVE your website! It's simply the best. I made this recipe a couple nights ago and it didn't turn out the way I envisioned. It was really gritty and just not quite mac and cheese like. I was wondering would have cooking the roux longer get rid of that problem? Thanks for your help! I'd love to make this again and hopefully get better results.
Assistant to 100 Days (Jill) says
Hi Ann. Did you use block cheese and shred it yourself? Sometimes if you use pre-shredded cheese it has a funny, "cake" like texture to it. Jill
Amy says
I just made this for my 3 year old daughter's birthday! She gobbled it up. It was SO GOOD!!!
Susan says
I followed the directions exactly but my cheese sauce was gritty. :( I shredded my own English Cheddar. I then tried it without the roux & just threw the cheese in with the hot noodles, some butter & milk, but still grainy. I've never had luck w/cheese sauce. Any suggestions?
Lisa says
I am sorry it didn't turn out. I would try whisking the milk in with the pan off the heat. Then return it to a low heat and keep whisking until you add the cheese. I hope that helps.
Michelle says
Freezes incredibly well! I froze individual portions in silicone muffin cups, popped them out when they were frozen, and they're in a gallon-sized bag in the freezer, ready for quick lunches (and breakfasts, which is what my son likes). My kids can microwave them for 1 minute or so whenever they want a snack, too. Way better than the individual cups (even organic) of mac and cheese at the supermarket. Wow!
Michelle says
Hmmm, this is the first thing I made from your blog that my family does not like. It tasted kind of sandy, and while it was very "saucy" it didn't taste cheesey enough.
Sarah says
I'm wondering how it would work to just freeze the sauce? It would be as easy (maybe easier) as boxed mac and cheese to cook some noodles, thaw and heat the sauce and throw it together. Awesome recipes! Thanks!
Assistant to 100 Days (Jill) says
Hi Sarah. Yes, I've frozen the sauce only before and it works fine if you heat it on low on the stove. Jill
Lindsay Amabile says
I made this tonight and my husband and I loved it! Definitely the best macaroni and cheese I've ever had! Thanks for sharing :)
Angela says
YUM! I added a little butternut squash puree just to get more veg in my reluctant eater - he gobbled it up and said, "This is the BEST!"
Michelle says
Made this yesterday and it gets a HUGE seal of approval from a kid who is not a picky eater, but is very particular about his mac and cheese because once he got sick after eating "non-boxed" stuff (total coincidence, I believe, but I have been unable to convince him of that). His exact words: "Mom, this is the best mac and cheese I have ever had." We'll be making it again on Thursday to take to a family who has meal needs due to hospital visits. Like literally every other recipe I've tried from her, it's simple and tasty - a perfect combo!
Courtney says
Also, next time I'll up the noodle count to 2 cups, but if anyone has the extra cheese sauce "problem" that I had, throw in some chickpeas! Definately the only way I've gotten my daughter to eat them in a loooooong time!
Courtney says
Pretty darn tasty. I made it with 100% almond milk, just to see how it would turn out, and it's very tasty although a tad sweet (and I'm using unsweetened original almond milk, so I'm not sure why...guess it's just the nature of the almond). I upped the salt content a touch and that seems to be working nicely against the sweetness, and I'll probably throw a little sriracha on mine :). I think next time I'll add a more potent cheese-I used a cheddar/parm/swiss combo today but will prob shoot to add in an asiago or gruyere next time, especially if I do the almond milk again so I wont have to do as much salt.
Thanks for the recipe!
Katie M says
Just found your blog about a week ago and I love love love it! I am trying to brainstorm make-ahead freezer meals for busy weeks. Have you ever tried to freeze your mac & cheese recipe? Thank you!
100 Days of Real Food says
I have not, but it might work...you should try experimenting with a small amount. Let me know!
Michelle says
I'm trying the freezing tonight. I've probably made this recipe 5 times in the past 2 weeks, and my son loves it. Tonight I'll freeze some in silicone muffin cups and pop the individual servings into a freezer bag once they're frozen, so he can microwave one whenever he's hungry. I'll let you know how it goes!
Anna says
This recipe is WAY better then macaroni and cheese from a box! It was perfect! I agree, NEVER use pre-shredded cheese because it's so hard to melt :(.
Caitlin says
Im 11 years old, and love to cook with my mom. She recently found this website, and we both love it! We just made this recipe, and it was AMAZING!!! Thank you sooo much for this awesome website and recipe! :)
Heather says
You might want to put a note on here to not use pre-shredded cheese. The declumping powder they put in the bags can cause the cheese to be grainy and not melt together well (i.e. separated strands of cheese)
Courtney says
Delicious! Whenever I walked past the blue boxes of Kraft macaroni I had to tell myself "It's processed. It's not good for you. Keep walking..." Now that I have this lovely recipe, though, it won't be a problem! It was a bit too creamy for me the first time, so the second time around I doubled the pasta and halved the sauce, and I'm enjoying a yummy bowl of it right now. :)
Christy says
Does this keep in the fridge well for leftovers? I'd rather make this once for dinner and have a couple of lunches from it too.
100 Days of Real Food says
Yes, you can store in the fridge, but to warm it up I would do it in a pan on the stove and add some extra milk or cream while it is reheating.
Sierra says
I've taken it for lunch and stuck it in the microwave several times now and it still tasted delicious!
Sierra says
Just made this and it was DELICIOUS! My boyfriend, who hasn't exactly been receptive to my dietary changes, also loved it! I used extra sharp white cheddar and whole wheat flour (not white wheat) and it was so creamy and good!
carissa says
I made this tonight and while it was good, my cheese sauce was grainy. Any idea what I need to do different next time? I'm really loving your site and recipes. I'm slowly cleaning out my kitchen and cleaning up our eating ;)
100 Days of Real Food says
Sometimes that can happen if it sits too long or the temperature isn't right. Did you follow the directions exactly?
Heather says
Make sure to shred the cheese yourself, pre shredded cheese has a declumping powder coating the cheese. If you didn't, you may have heated the cheese too long until it "broke"
Assistant to 100 Days (Jill) says
The FAQ, specifically number 6, addresses the type of cheese Lisa and her family use. You can find it here: https://www.100daysofrealfood.com/frequently-asked-questions/
Jessica says
I made this the other night, but instead of pasta (we were out) I used quinoa instead. It was awesome! Kind of like a cheesy "grits". Your cheese sauce recipe is wonderful. Thanks for your website...many of your recipes have become staples in our household!