Cheesy Baked Spaghetti Squash

A bowl of Cheesy Baked Spaghetti Squash.


It's not all that often that I post recipes containing dairy on here anymore, but this Cheesy Baked Spaghetti Squash is gluten-free, full of cheese and it's delicious. I used to consume more cheese when I was following the SCD diet which I know a lot of my readers still are, so this one is for you. It is also for all of you who are Paleo or Primal and occasionally enjoy dairy, like myself.

Dairy is something I have found I can tolerate once or twice a week and as long as it is low in lactose, such as harder cheeses and the farmer's cheese I use in this recipe. I also have a much better tolerance for raw cheeses or sheep and goat's milk cheeses. Milk and cream are still untouchable, even if fermented in yogurt or keffir, but I am ok with that and love that I can still enjoy cheese from time to time. If you are fully dairy-free, try using my nut cheese from my book as a replacement in this recipe!


CheesyBakedSpaghetti-Against all Grain


Funny enough I actually just found this post pending from the time when I was writing my cookbook. I guess time got away from me in this instance and I completely forgot to share it with you! The original recipe came from a menu planning site that I used to use before switching my diet. I altered it to fit my grain-free needs and it is the quintessential comfort dish. Plus you can prepare a second one and freeze it before baking it for a night when you are completely out of time and need something easy to pull out!


CheesyBakedSpaghetti from Against all Grain

Cheesy Baked Spaghetti Squash



Cuisine: Italian

Category: Dinner

PREP TIME: 15 mins

COOK TIME: 60 mins TOTAL TIME: 75 mins


  • 1 medium spaghetti squash about 3 lbs, baked al dente (slightly undercooked from the directions linked)
  • 1 tablespoon ghee or olive oil
  • 1/4 cup yellow onion, finely minced
  • 2 garlic cloves, minced
  • 1 pound ground beef or uncooked Italian chicken sausage
  • 2 cups tomato puree
  • 1/4 cup water
  • 2 tablespoons tomato paste
  • 3/4 teaspoon parsley
  • 1/2 teaspooon oregano
  • 1/4 teaspoon red pepper flakes
  • 3/4 teaspoon sea salt
  • 1/4 teaspoon cracked pepper
  • 1 cup ricotta (use farmer’s cheese for SCD)
  • 1 cup shredded raw mozzarella or smoked fontina cheese
  • 1 egg, beaten
  • 3 tablespoons freshly grated parmesan


  1. Preheat oven to 350 degrees F.
  2. Heat the ghee in a large saucepan over medium heat. Add the onion and garlic and sauté until translucent, about 5 minutes.
  3. Add the meat and brown until cooked through, about 7 minutes.
  4. Pour in the tomato puree, water, tomato paste,  parsley, oregano, red pepper flakes, and sea salt. Simmer for 10 minutes.
  5. Shred the ‘noodles’ of the spaghetti squash with a fork and transfer them to the pot with the sauce and meat.
  6. Add the farmer’s cheese, shredded fontina, and egg and stir to combine.
  7. Lightly grease a 9×12 casserole dish with ghee or olive oil then pour in the spaghetti mixture and spread evenly.
  8. Bake in the oven for 20 minutes. Add the parmesan cheese on top then bake for an additional 12 minutes, until bubbly and the cheese has browned slightly on top.


  • The spaghetti squash can be prepared up to 3 days in advance. The entire casserole can be assembled the day before being baked and stored in the refrigerator, or prepared and frozen for 3 months. Thaw in the refrigerator for 24 hours before baking.
  • To save time, you can purchase a good quality jar of marinara sauce. Look for one that does not have additives, sugar, or citric acid. Omit ingredients 6-12 if doing so.
  • For dairy-free, substitute out all of the cheese for 2 cups of the nut-cheese from page 304 of Against all Grain

Keywords: egg free, gluten free, main dish, nut free, scd, vegetarian, Italian