This delicious Keto Chili Casserole has a spaghetti squash base and is loaded with cheese, ground beef chili, and sour cream. It’s a saucy chili masterpiece that the entire family will love! Low carb and gluten free too!

Note: there is a 1 minute video for this keto chili casserole recipe so be sure to watch it and see how quick and easy it really is!
Raise your hand if you love cheese! Just kidding, put it down….you know I can’t really see you right???
Don’t worry though, I know how you feel. I felt your fervent love of cheese from all the way over here. Because who doesn’t love cheese? Even people who can’t eat cheese WISH they could.
What’s not to like, really? Cheese makes everything better, and that’s a fact.
Recipes containing cheese practically write themselves because I can literally start with cheese, open my fridge and grab 5 other random things to add to that cheese and BAM! Delicious.
I put a little more effort into it than that for this keto chili casserole recipe, but not much (shhh, don’t tell anyone.)

My one caution about buying pre-shredded cheese for this keto chili casserole is that you should be aware that all shredded cheese has added starch to coat the shreds and keep them from sticking together in the package. That can add a gram or two of carbs per serving, so if you are on a very low carb diet like keto (20g or less) you may want to opt for the block and shred it yourself at home.
Another option is sliced cheese – I sometimes just layer the slices in a keto casserole recipe like this one, or the Easy Cheesy Cauliflower Gratin, which uses slices of pepper jack cheese. Loaded with flavor and super easy to throw together, you definitely need to check that keto cauliflower recipe out if you haven’t already!
This cheesy keto chili casserole recipe has a spaghetti squash base, then a layer of cheese, a layer of sour cream, a layer of chili, and then more cheese (of course.) It’s hearty and satisfying, but not so heavy that it will weigh you down.

I like mine sprinkled with cilantro, but that’s completely optional. You can also serve this keto chili casserole alongside some salsa, additional sour cream, and guacamole or slices of avocado.
Whether you eat this tasty keto chili casserole as is, or garnish it with your favorite chili toppings, this one is going to be a hit with the whole family!
More family friendly keto dinner recipes:
Peruvian Chicken with Green Sauce
Keto Chili Casserole – Low Carb
- Total Time: 45 minutes
- Yield: 8 servings 1x
- Diet: Diabetic
Description
A keto chili casserole recipe loaded with chili, sour cream, and cheese on a spaghetti squash base. Easy to make and family friendly!
Ingredients
For the chili:
- 1 lb lean ground beef (or turkey)
- 1 teaspoon ground cumin
- 1 teaspoon ground coriander
- 1 tablespoon chopped chipotles in adobo (optional)
- 1/2 teaspoon garlic powder
- 1 teaspoon dried oregano
- 1/2 cup prepared salsa
- salt and pepper to taste
For the casserole
- 4 cups cooked spaghetti squash
- 2 tablespoons butter, melted
- 3/4 cup sour cream
- 1 3/4 cup shredded cheddar cheese
- chopped cilantro (optional)
- sour cream, salsa, avocado to serve (optional)
Instructions
For the chili:
- In a medium saucepan brown the ground meat seasoned with salt and pepper.
- Pour off any extra fat and discard.
- Add the rest of the chili ingredients and simmer for about 10 minutes.
For the casserole:
- In a medium bowl combine the cooked spaghetti squash and melted butter, tossing to coat.
- Season generously with salt and pepper to taste.
- Spread the squash out in a 12 – 14 inch casserole dish.
- Sprinkle with 3/4 cup of shredded cheese.
- Spread the sour cream over the cheese layer.
- Spoon on the chili and spread it out, leaving a 1 inch border of spaghetti squash around the edge.
- Top with the remaining 1 cup of shredded cheese.
- Bake in a 350 degree oven for 30 minutes or until heated through.
- Sprinkle with cilantro and serve with sour cream, salsa, and guacamole or avocado slices as desired.
- Prep Time: 15 minutes
- Cook Time: 30 minutes
- Category: keto dinners
- Method: Stovetop
- Cuisine: Mexican
Nutrition
- Serving Size: 1.5 cups
- Calories: 284
- Fat: 20g
- Carbohydrates: 6g net
- Protein: 23g
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Dede Petty says
Hi Mellissa,
I am just starting on my Keto journey. Have finished my 3 Day Kickstart. Now I am advancing on to the next step… My question… This CHEESY CHILI SPAGHETTI SQUASH CASSEROLE looks DELISH and I want to try it. My problem…I am allergic to any squash that is not orange. Many recipes I have run across use squash in them. What can I substitute that would not ruin the flavor of your dish?
Mellissa Sevigny says
Try it with zucchini noodles!
Dede says
Oops! Zucchini is also a squash. I am highly allergic to. Have you tried to make noodles from Butternut or Acorn that have orange flesh? I don’t see any recipes using these squashes.
Looks like it is time for me to do some experimenting! (;
Mellissa Sevigny says
You could but but of those are high in carbs and wouldn’t be suitable for a keto or low carb diet. If you aren’t concerned with carbs then those squashes would be fine.
Kathy says
If you can’t use summer squashes, it would seem that shredded cabbage would be a good sub.
Melissa says
What about using cauliflower, minced, with butter? Like the cauliflower rice? That could probably form to the pan to sort.
greg k says
This recipe was so good, I did use a hot salsa to amp up the spiciness. Definitely a new staple in my house. The only hard part is sticking to a 1.5 cup serving.
Stephanie says
My whole fam is obsessed w/ this one. thank you so so so much!
Mellissa Sevigny says
We are too, thanks Stephanie!
Michele says
I can’t believe it took me until I was 50 to try spaghetti squash. This recipe is absolutely delicious. I’m keeping this one for myself, but the next time I make it I’ll have to double it so I’ll have some left over for me. My son and husband will gobble it down:)
amy says
Easy! Delish! My kids ate it right up too. I put black olives on top of mind and figured them into my macros. Otherwise made as written. Yum. Will definitely make again. Thanks!
Lindsay says
Hi Mellisa! I am wanting to try this tonight however I’m wondering if you used a pie dish to bake this in? It looks so pretty in the pictures…
Jvcl888 says
I’ve made this several times and my family loves it! I have a little trouble with it being runny though. Should I do something different to the spaghetti squash to make it less moist? When I cook the squash should it be pretty mushy or still have some crunch?
Thanks!
Mellissa Sevigny says
You want it to be tender, not mushy because it will continue to cook when you bake it. Make sure you are draining the squash thoroughly before putting it in the casserole pan!
Jvcl888 says
Thanks!
Nina says
Hi! Could this be done in crock pot?! Thanks so much!!
Mellissa Sevigny says
Theoretically yes, but I worry that the squash would turn to mush – let us know if you try it!
Debi says
This was so delicious!! I made it this week and ny husband loved it so much that I’m making it again this week!! We both started your week one plan last week, and we both love it!! Looks like we’ll be repeating week one since my husband wants this casserole again :). Thank you for all your hard work in laying everything out for us. You’ve made it so very easy!!
Gail says
This is the first one of your recipes I have tried, and it was delicious! Even my husband, who is “meat and potatoes”, liked it. Thank you. Looking forward to trying more!