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Preheat oven to 400 degrees F.
Cut both spaghetti squash in half and remove the seeds (scoop them out with a metal spoon).
Brush the inside with olive oil (or spray with an olive oil spray) and sprinkle with sea salt and pepper.
Place cut-side down in a baking dish.
Fill baking dish ¼” with water.
Cover baking dish with aluminum foil.
Bake in the preheated oven for 45-60 minutes or until the squash is soft to the touch (it will compress down when pushed lightly).
Remove from the oven and turn the cut-side to the top.
Use a fork to shred the spaghetti squash, being careful not to poke holes in the shell.
Leave shredded spaghetti squash in the shell while you make the cheese sauce.
Preheat oven to 375 degrees F.
In a small bowl, combine flour sea salt and garlic powder. Set aside.
Melt butter in a medium saucepan over medium heat.
Add dry ingredients and whisk to combine.
Whisk constantly until ingredients just start to brown (about 1-2 minutes).
Add milk and whisk until mixture is smooth.
Continue cooking over medium-high heat until the mixture comes to a boil and starts to thicken (about 3-5 minutes).
Once mixture is thick, add 2 cups of shredded cheese and whisk until the cheese is completely melted.
Once cheese sauce is smooth, remove the saucepan from the heat.
Distribute cheese sauce evenly among the four halves of shredded spaghetti squash (with the size squashes I had, I used about ½ cup plus 2 TBS of cheese sauce for each of the four halves).
Use a fork to gently stir the cheese sauce into each half of shredded spaghetti squash.
Once the sauce is evenly distributed in the squash, use the fork or a spatula to smooth out the surface of each squash half.
Top with remaining ½ cup of cheese and bake in preheated oven for 15 minutes, or until the cheese on the top is melted and lightly brown.