Preheat oven to 400 degrees F/205 degrees C. Line a baking sheet with parchment paper and set aside.
Carefully slice open the spaghetti squash in half lengthwise. Scoop out the seeds and discard.
Rub the flesh with olive oil, and sprinkle with salt and pepper.
Place the two halves flesh side down on the prepared baking sheet. Bake for 25 to 35 minutes until the strands can be pulled away from the sides with a fork but are still crunchy. I like to slightly undercook the squash so that it doesn't get waterlogged and cause the sauce to get watery.
When the squash has finished cooking, use an oven mitt to flip the squash over and handle them while you pull the strands away. Reserve the empty halves for stuffing them later.
Put the chopped baby spinach and spaghetti squash strands to a large bowl. Stir so that the steam from the squash wilts the spinach. Let it cool slightly while you make the sauce.
Warm olive oil in a large skillet over medium heat. Add the onion and cook for 3 minutes until it starts to soften. Stir in the garlic and cook for another minute until fragrant. Remove from heat.
Transfer the cooked onion and garlic to a high-speed blender. Add the white beans, cottage cheese, parmesan cheese, lemon juice, salt, and pepper.
Blend on medium until smooth. If needed, add milk, just 1 tablespoon at a time, to promote blending. You want the sauce to be pourable but still quite thick. The steam from the spaghetti squash will contribute liquid, and if there’s too much milk/liquid in the sauce to begin with, it will get too watery when added to the squash.
Pour the alfredo sauce from the blender into the same skillet you used to cook the onion and garlic. Heat over low heat (important), stirring often, for 60 to 90 seconds until just heated through. Promptly remove from heat. This warms up the sauce enough so that it doesn’t have thermal shock when combining with the spaghetti squash, which would cause separation. It's important not to boil the sauce in the skillet or else it will separate that way.
Pour the gently warmed sauce over the slightly cooled squash and spinach. Stir until coated.
Divide the spaghetti squash mixture evenly between the remaining empty halves.
Sprinkle each half with the remaining parmesan cheese.
Turn the oven to the broiler setting, and bake the filled squash halves for 1 to 3 minutes until the cheese is melted and lightly browned.
Remove from the oven, and serve warm!
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