Twice Baked Spaghetti Squash with Spelt | @naturallyella

I was slow to warm up to spaghetti squash. I had fallen in love with the smooth texture of acorn and butternut squash. Spaghetti squash was different and highly unappealing. However, my thoughts have changed and I now like to use the unique texture to my advantage. This twice baked spaghetti squash is a little on the time consuming side of cooking but it’s a great alternative when you’re not feeling mac and cheese. Cook the spelt and squash ahead of time, this will greatly speed up dinner!

Twice Baked Spaghetti Squash with Spelt | @naturallyella

Twice-Baked Spaghetti Squash with Spelt

  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 2 servings
  • Category: vegetarian main course


A hearty take on mac and cheese using spaghetti squash and spelt in place of traditional noodles.


  • 1 spaghetti squash (halved and cooked)
  • 1 cup cooked spelt
  • 1 tablespoon unsalted butter
  • 1 small shallot
  • 1 tablespoon flour
  • 3/4 cup whole milk
  • 1/2 cup cheddar cheese (plus extra for topping)
  • 1/4 teaspoon salt
  • 1/4 teaspoon black pepper
  • 1/2 cup panko
  • Chives, for serving


  1. Heat oven to 400˚F. 
  2. In a small pot, melt butter over medium-low heat. Add the shallot and saute until translucent and fragrant, 4 to 5 minutes. Add in the flour and cook for one minute. Measure in milk, salt, and pepper. Let cook until thickened, stirring often. Remove from the heat. Add in the cheese and stir until cheese has melted.
  3. Scrape out the squash into a bowl. Stir in the spelt berries and add the cheese sauce to the bowl. Stir until everything is well combined. Divide the mixture back into to two halves of the spaghetti squash. Sprinkle the tops with the panko and extra shredded cheese.
  4. Bake the squash until the cheese is melted and the panko has browned, 25 to 30 minutes. Sprinkle with chives before serving.


Tips & Tricks: To cook the spaghetti squash: cut in half, remove the seeds, and place upside down in a pan. Add ¼” of water and roast until the squash is tender.

Stock up: get the pantry ingredients you will need: panko, spelt

Nutrition: see the information. 


  • Calories: 462
  • Sugar: 12.1
  • Sodium: 856
  • Fat: 20.6
  • Carbohydrates: 56.5
  • Fiber: 8
  • Protein: 18.1
  • Cholesterol: 53.2

Twice Baked Spaghetti Squash


There’s not a lot going on in this twice baked spaghetti squash outside of the squash and the cheese base. You can easily swap out the grain or make this gluten-free. A few ideas:

Greens:Stir in a couple handfuls of spinach before adding the spaghetti squash mixture back to the squash halves. I prefer spinach because it wilts the easiest.

Grains: Another hearty grain like spelt would work such as einkorn, farro, sorghum, wheat berries.

Gluten-free: Use a gluten-free grain that would hold up to the cooking process, like sorghum or oat groats. Also be sure to use gluten-free breadcrumbs or just plan to leave those out.