Kicked up with chipotle peppers and bacon and made extra-creamy from butternut squash, this bacon chipotle mac and cheese is packed with bold flavors!
Just to preface a little bit, you are probably either going to hate me or love me after we’re through with this post. And it’s all this mac and cheese’s fault.
Or to be more specific, blame the bacon, chipotle, and all the 10034 other things I packed into one innocent pan of mac.
This mac and cheese is definitely more on the unique side with all of its additions but TRUST ME, it absolutely works.
Creamy butternut provides a little extra texture alongside the pasta and then we’ve got smoky bacon and spicy chipotle coming in to provide ALL the flavor.
Really just a panful of cheesy perfection that everyone needs in their face.
This Mac and Cheese features…
- A rich and cheesy chipotle cheddar sauce
- Crispy bacon bits and tender butternut squash cubes
- A crunchy panko breadcrumb topping
Making the Mac and Cheese
(scroll down to the bottom of the post for the full recipe)
Ingredients You Will Need
- Butternut squash
- Bacon
- All-purpose flour
- Garlic
- 2% or skim milk
- Heavy whipping cream
- Chipotle in adobo sauce
- Cheddar cheese
- Pepper jack cheese
- Pasta
- Panko breadcrumbs
- Unsalted butter
Choosing Your Pasta
This mac and cheese works well with a variety of pasta shapes but I recommend sticking with a shorter cut. Try spiral, penne, shells, elbows, rigatoni, or ziti.
Tips for Perfect Mac and Cheese
- Boil butternut squash – cook the squash in boiling water 8-10 minutes until fork-tender.
- Mash butternut squash – no need to get it perfectly smooth, you want a few chunks for extra texture in the mac and cheese.
- Make a roux with bacon drippings and butter – a roux is equal parts fat and flour and it is the base to your sauce. Cook the roux over medium heat, whisking constantly until a light golden brown.
- Slowly drizzle in milk + cream – use a whisk to evenly incorporate the liquids into the roux to avoid lumps
- Cook sauce over medium heat – once the milk and cream have been added, cook the sauce over medium heat and stir often to avoid burning. The sauce is done when it’s bubbly and can coat the back of a spoon.
- Fold in cheese offheat – this will prevent the cheese from burning. Once the sauce is thickened, remove from heat and whisk in cheese until melted.
- Cook pasta to al dente – be careful not to overcook your pasta during boiling as it will continue cooking a bit once added to the sauce.
- Top mac and cheese with breadcrumbs and bake – 400F 15-20 minutes will crisp up the breadcrumbs beautifully.
Recipe Variations
Try these ideas for a different twist on this mac and cheese.
- Use another squash – try delicata or acorn squash in place of the butternut.
- Swap cheeses – try mozzarella, gouda, Parmesan, or gruyere.
- Adjust heat level – use 1 tablespoon chipotle for a mild version. Alternatively, start with the suggested 2 tablespoons and work your way up to taste.
- Try another meat – replace the bacon with about a cup of shredded chicken or browned sausage. You can also skip the meat entirely.
The smoky chipotle paired with all that gooey cheese and creamy butternut squash really just works in this glorious pan of mac! Don’t tell anyone but I like to sprinkle my bowl with a little extra crispy bacon for obvious reasons.
Mac and cheese has never been so dang fun!
Save this recipe using the ‘save to recipe box’ button below. If you make it, please let us know! Leave a comment + star rating below, or take a photo and tag it on Instagram with #wholeandheavenlyoven.
You’ll love these other mac and cheese recipes!
Bacon Chipotle Mac ‘n’ Cheese
This recipe may included paid links. As an Amazon Associate, I earn a commission from qualifying purchases.
Ingredients
- 2 cups butternut squash, cut into 1/4-inch cubes
- 4 strips bacon
- 3 tablespoons unsalted butter, divided
- 4 tablespoons all-purpose flour
- 2 medium cloves garlic, minced
- 3 cups 2% or skim milk
- 1 cup heavy whipping cream
- 3 tablespoons minced chipotle in adobo sauce
- 1-1/2 cups shredded cheddar cheese
- 1-1/2 cups shredded pepper jack cheese
- 12 oz pasta (spiral, penne, shells, etc) cooked according to package instructions until al dente
- 3/4 cup panko breadcrumbs
Instructions
- Preheat oven to 400F and lightly grease a 9-inch baking dish. Set aside.
- Bring a medium pot of water to a boil over high heat. Reduce heat to medium, add butternut squash, and allow squash to simmer 8-10 minutes until tender when pierced with a fork. Drain squash, transfer to a bowl, and lightly mash with a fork into a semi-chunky mash. Set aside.
- Arrange bacon in a single layer in a large skillet over medium heat. Cook bacon 8-10 minutes, turning occasionally until bacon is crispy. Drain bacon on paper towels then finely chop.
- Set pan with bacon drippings over medium heat and melt 2 tablespoons butter. Whisk flour and garlic into drippings and cook 1-2 minutes until golden-brown.
- Slowly drizzle in milk and cream, whisking constantly until smooth and incorporated. Cook sauce over medium heat, stirring occasionally until sauce is bubbly and thickened. Remove from heat and add chipotle and both cheeses, stirring until cheese is melted.
- Fold cooked pasta, butternut squash, and bacon into sauce and season with salt and pepper to taste. Scrape pasta into prepared baking dish and set aside for a moment.
- In a small bowl, combine breadcrumbs and melted butter. Sprinkle evenly over mac and cheese.
- Bake mac and cheese at 400F 15-20 minutes until sauce is bubbly and breadcrumbs are golden-brown. Serve mac and cheese warm and enjoy!
Notes
Nutrition
This post was updated with new recipe adjustments and photos on 2/12/26.
Gayle @ Pumpkin 'N Spice says
I wish I could reach through my screen and grab a bowl for breakfast! I’ve been seeing butternut suash mac ‘n cheese everywhere lately, so I need to try some! Your version with bacon sounds SO good!
Sarah says
I’m SO down with this mac ‘n’ cheese being breakfast! Why didn’t I think of that?? 😉 Thanks Gayle!
Chelsea@RunningWithaWhisk says
Ha! I love that you mentioned we WILL eat a lot of this if not the entire pan. I am powerless over a big bowl of mac ‘n cheese. This recipe looks absolutely fabulous!
Sarah says
Right?? The mac ‘n’ cheese struggle is REAL! 😉 Thanks Chelsea!
Jen | Baked by an Introvert says
I am a pasta-holic! Butternut squash, chipotle, and bacon are an irresistible combo in mac ‘n cheese. I’m dying to have this for breakfast right now.
Sarah says
I’m right there with ‘ya on being a pasta crazy lady. 😉
Kristen @ The Endless Meal says
Holy damn, girl! You’ve just managed to put all my favourite things into one delicious title. This sounds incredible!
Sarah says
Haha! Thank you so much girlie! xoxo 🙂
Mary @ LOVE the secret ingredient says
Squashes and sweet potatoes are always one of my favorite pairings with bacon! And I have to say chipotle and cheese are very welcome additions to the mix!
Sarah says
Anything goes with bacon, right?? Thanks Mary!
marcie says
I love butternut squash mac ‘n cheese, and I think adding bacon and chipotle to the mix can only make it better (maybe about 100 times better)! This looks so creamy and delicious, Sarah!
Sarah says
Aw thanks so much Marcie!!
Ashley says
Chipotle peppers are just the best! I love their smokiness! And this mac and cheese sounds fantastic – especially with the butternut squash!!
Sarah says
Oh gosh, YES! The smokiness is the best part about chipotles!
mira says
Definitely not in the “hate you” camp! Love mac and cheese and have been thinking to make some! This looks perfect, packed with awesome ingredients! Pinning!
Sarah says
Yay!! Thanks Mira! I hope you love it!
Annie says
Gimme all that cheesy carby goodness!! Yes!!
Sarah says
Thanks Annie! xoxo
Amanda says
Those chipotle chilies sound so good in this Mac and Cheese. I’m afraid to try this because I might eat the whole pan myself. ? Is that a bad thing?
Sarah says
Haha! It’s definitely a distinct possibility, but TOTALLY worth it!
Rachel @ Bakerita says
I am FIRMLY in the “love you” camp right now, especially as I drool all over this delicious mac and cheese. I’m totally making a big dish of this ASAP. That cheesy goodness is calling my name…loudly.
Sarah says
Woot! You will totally love this mac, Rachel! LMK how it turns out!
Anne says
This looks absolutely wonderful!!! Can I please stuff the whole thing in my mouth??(Don’t judge me…)
Sarah says
Haha! NO judgement from me, because I kinda did the same thing!
Anne says
This looks absolutely wonderful!!! Can I please stuff the whole thing in my mouth??(Don’t judge me…)