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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Elissa says
This was SO GOOD! I haven’t made spaghetti squash in years because it’s so difficult to cut (and it was a lot of work cutting it for this recipe) but now that I see Melissa’s post on how she cooks her spaghetti squash, I will definitely try that way next time. My 12 year old said “I think the noodles are a little undercooked” tee hee. He didn’t even know it was squash until I told him. Will definitely be adding this to the rotation!
Tracy says
This was absolutely fantastic! Will be making this over and over again.
donna says
hi! Thanks so much for these recipes. They are fantastic. I have a question about serving sizes – although I’m following your recipes exactly, when I measure out the portions (I portion it out at once!) I am ending up with serving sizes that are smaller than what your recipes say – for this one, I got serving sizes of about 1 cup, not 1 1/2 cups. Do you have any advice for me?
Mellissa Sevigny says
Hi Donna, not really sure why you’re getting less than I did when I measured it. Could be that mine had more moisture in it which bulked it up – it’s hard to say. If yours are a little different than mine even though you follow the recipe exactly, then just portion into the called for number of servings and that should be the right nutrition info per serving, even if it’s a little more or less than the serving size estimates. Thanks!!!
Ilyse says
OMG…yummo!! I am such a fan of all of your recipes, and this one is right up at the top of my list of faves!
Lisa says
My children do.not.like. squash of any kind. My husband likes squash but wanted me to do something different with the spaghetti squash I had instead of just the typical replacement for spaghetti noodles. This dish was SO good! Even my children liked it. I couldn’t believe it! I will definitely be adding this to our rotation. Thank you!
Mellissa Sevigny says
YES! I’m always happy when my recipes can get sworn squash or cauliflower haters to convert – especially when it’s kids!!!! So glad they liked it, thanks for letting me know!
Stephanie says
You don’t even know how much I love this. The best spaghetti squash recipe I have ever had. Bravo!
Mellissa Sevigny says
Being that there are SO many spaghetti squash recipes out there – hooray!!!!! So glad you liked it and thanks for letting me know! :)
Valerie says
This Is Wonderful! Even My Hubby Loved It!!
Kim Beaulieu says
I need this in my life. Like right now. Like 10 minutes ago.
Mellissa Sevigny says
You DO! You really really do!!!!
Carol Carlton says
This sounds super yummy!
Just wanted to call your attention to the fact that I have not been able to ‘pin’ this or a couple of other of your blog recipes of late. They won’t ‘pin’ from your page pin links or my own.
Mellissa Sevigny says
Thank you Carol, I have found that they pin sometimes and then other times they won’t and it’s very frustrating because I can’t figure out why. My hosting company says it’s not on their end, it might be cloudflare, but it’s definitely hurting visibility and traffic on my newer posts. I’ll keep working on it – thanks!
Carol Carlton says
Success! Pinned this! :)
Mellissa Sevigny says
Thanks for letting me know Carol – hopefully this issue is resolved for good!!!
Carlos Gato says
interesting recipe, can’t wait to try it out. Quick question. How do you cook the spaghetti squash?
Mellissa Sevigny says
Carlos I microwave mine whole (after piercing it a bunch of times) for about 20 minutes, then I let it cook for about 10 before I split it open, remove the seeds, and scoop out the squash. It’s easy and it works great! Enjoy!
Carlos Gato says
thanks Mellissa worked like a charm, recipe was delicious!
Tom says
ok im microwaving the squash for 20 minutes. Questions how do you cook it for the additional minutes? In stove? How? sorry
Mellissa Sevigny says
You mean after you make the casserole? Then you bake the whole thing. Otherwise not sure what you’re asking! 20 minutes in the microwave should be plenty to get it soft enough to scoop out, but if it isn’t just hit it for another 5 minutes in the microwave.
Vicki jackson says
I am a little confused by your explanation. You said you microwave for 20 minutes then cook 10 minutes. How are you cooking it the 10 minutes? I’ve never purchased spaghetti squash so how many do I need for this recipe? New to this way of eating but have heard lots of great things about your recipes. Thanks for your help.
Anon says
Your explanation is confusing. You stated that 20 minutes is sufficient enough, but to continue cooking it for an extra 10 minutes before you “split it open, remove the seeds, and scoop out the squash”.
Rachael says
I am reasonably certain the second “cook” was a typo for “cool.” Cook it for 20 minutes, then let it cool for 10.