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Spinach + Cheese Baked Spaghetti Squash

Active Time: 15 minutes
Total Time: 75 minutes
  • Gluten Free
  • Vegetarian
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Why we love it:

Fast recipes almost always either take a long time to cook but require little prep OR require tons of chopping and are very simple. This one is definitely the former. It’s seriously so easy to toss together but it needs time in the oven. You can prep these a day ahead and just bake off the next night too, which makes life super simple.


  • 1 Spaghetti Squash (or 2 if they’re small and you want each person to have their own)
  • 1 head Garlic
  • 12 cup Heavy Cream (or half & half or whole milk)
  • 8 ounces Frozen Chopped Spinach (thawed and squeezed)
  • 1 teaspoon Dried Thyme
  • 4 ounces Fresh Goat Cheese
  • 112 cups Mozzarella (shredded)
  • 12 teaspoon Red Pepper Flakes (to taste)
  • 1 Red Bell Pepper (small)
  • 1 Shallot
  • 2 teaspoons Extra Virgin Olive Oil
  • 2 teaspoons Kosher Salt (divided)
  • 12 teaspoon Black Pepper (divided)
  • 12 cup Parmesan Cheese (grated, divided)
  • 1 Tablespoon Unsalted Butter (room temperature)

Cooking Instructions

  • 2. SQUASH

    Put the whole spaghetti squash as is (no sticker!) in the microwave for 6 minutes on high. Remove carefully, it will be hot!

    Slice a tiny bit of the stem end off. Slice in ½ lengthwise. Use a spoon to scoop out the seeds and pulp, place the halves cut side up in a casserole dish.

  • 3. GARLIC

    Slice off the top portion of the garlic head to expose some of the cloves. Place both halves next to the squash in the dish.

  • 4. FILLING

    In a medium bowl, mix together the goat cheese, milk, spinach, thyme, and mozzarella. Season with red pepper flakes, and 1 teaspoon of salt and about ¼ teaspoon pepper.

    Slice the bell pepper thinly and slice the shallot thinly. Add both and mix with the cheese.

  • 5. STUFF

    Poke the insides of the cleaned squash with a fork, all over. Drizzle with olive oil and sprinkle 1 teaspoon of salt and ¼ teaspoon of pepper on the squash. Cover this with most of the parmesan - reserve a Tablespoon or so.

    Divide the spinach and cheese mixture between the halves and pack it into place. Top with reserved parmesan. Cover with foil and bake for 35 minutes.

    Remove the foil and continue baking for another 15 - 20 minutes or until the squash is tender and the cheese is golden brown on top.


    Let the garlic cool a bit, then squeeze the cloves out into a bowl. Add the butter and mash together. Dollop on top of the squash halves.

  • 7. SERVING

    If large and feeding 4, cut squash directly in ½ and plate. Use a fork to scrape the squash into strands, mixing the cheese with the squash.

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    use your favorite cashew or other non-dairy cheese. Or omit the cheese and just make it veggie packed, you can add a dash of soy sauce over top for depth. Use broth, stock or water instead of milk
    double the goat cheese and omit mozzarella cheese. Use pecorino instead of parmesan. Use non-dairy milk instead of whole milk
    you can mix up and swap out the spinach, peppers, and shallot as you please. Try mushrooms, artichokes, other leafy greens, corn, peas, etc.
    add par-cooked ground sausage or turkey to the cheese mixture

Kid Friendly Version

How to Tweak This Recipe for Kids:

  • Plain spaghetti squash with marinara is delicious! Cook an extra squash and just scrape out the strings, top with sauce and cheese. If this might be too much, you can even mix this 50/50 with boiled spaghetti
  • Or try stuffing the squash like pizza. Spoon in store bought pizza or pasta sauce and top with mozzarella. Bake in the same way
  • Consider omitting red pepper flakes

For Toddlers

  • Omit a bit of cheese if it’s too much for you. To serve, before adding the garlic butter, just scrape out some of the filling and chop it up finely
  • Omit or swap ingredients that are too much - perhaps just bake on with some cheese, spinach and pepper

For Choosy Eaters

  • Try simplifying the filling (just a bit of spinach and mozzarella?) and baking a bit over top of plain regular spaghetti or pasta
  • Or bake an unstuffed squash and scrape out the strings and serve with marinara
  • Or stuff the squash with a simple sauce they do like - pesto? Or just cheese like mac and cheese
  • Fill plate with fruit and veggies

Prep Ahead & Use It Up

  1. Par-bake (aka microwave) the squash and scoop out the seeds. Wrap tightly and use within 3 days
  2. Mix up the filling. Store for up to 2 days
  3. OR do both steps 1 and 2 and stuff the squash. Wrap tightly and bake within 30 hours or so for best results (it will just start to get watery, no health risk in waiting longer)
  4. Leftovers are amazing. Either reheat in the oven OR scrape everything out of the squash skin and mix it up. Serve this in a bowl over rice or quinoa, or on a piece of crusty toast

Culinary Skills

Instead of microwaving the squash, you can just cut it in ½ and start baking. It may take an extra 10 – 20 minutes though. In general, you can fully microwave cut squash in a casserole dish. Fill dish with 2 inches of water and place squash in, cut side down. Power on high for 14 – 19 minutes or until tender. Scrape out squash to use in any other recipe. Freezes great!

Rate this recipe:
3 votes, average: 5.00 out of 53 votes, average: 5.00 out of 53 votes, average: 5.00 out of 53 votes, average: 5.00 out of 53 votes, average: 5.00 out of 5 (3 votes, average: 5.00 out of 5)
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