Twice-Baked Butternut Squash

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Winter squash was never one of my favorite vegetables. Even the fall favorite, pumpkin, just didn’t do it for me. Pie, puree, latte, I just wasn’t having it. But when you embrace a whole-foods diet like the autoimmune protocol, it’s a bit more fun if you do it with a sense of adventure. So, every fall, I try to find at least one new way to cook squash that actually makes me want to eat it.

A recent run-in with my mom’s twice-baked potatoes (a holiday staple for her) got me thinking… why not twice-bake other starchy vegetables? Combined with coconut milk and a few simple fall seasonings, this butternut squash comes out a creamy, melt-in-your-mouth puree vaguely reminiscent of pumpkin pie. You can even skip the coconut topping and serve it with a dollop of whipped coconut cream instead!

5.0 from 1 reviews
Twice-Baked Butternut Squash
Prep time
Cook time
Total time
Serves: 4 servings
  1. Preheat the oven to 350 degrees F. Place the squash halves cut-side down on a baking sheet, and roast for 60-90 minutes, until the flesh is easily scooped out of the skin with a fork.
  2. Raise the oven to 425 degrees F. Remove the flesh from one of the squash halves and set the flesh aside, discarding the shell. Hollow out the remaining squash half, leaving about ¼ inch of flesh attached to the skin so that the squash will keep its shape.
  3. Combine all of the removed flesh with the remaining ingredients except coconut in a blender. Puree until well-combined.
  4. Pour the puree into the hollowed-out squash half and sprinkle with coconut flakes.
  5. Bake 5-10 minutes, or until golden-brown on top.


About Christina Feindel

Christina Feindel came to the AIP after she was diagnosed with Hashimoto's, Celiac, and Interstitial Cystitis in her early twenties after more than a decade of declining health. As her degenerative and debilitating symptoms began disappearing, Christina began sharing recipes and experiences at A Clean Plate and is now the author of several healthy e-books. Christina believes that good, healthy food should be accessible and appealing to anyone on any budget, with any amount of time, and with the bare minimum of ingredients. She also believes that any illness can be improved or even eliminated by starting with a clean plate. You can find her on Facebook, Instagram, Pinterest, and Twitter.


  • Judy says

    I am getting very frustrated as I find that most of the recipes have coconut oil, coconut butter or coconut in them and I am sensitive to coconut and can no longer eat it (at least not for 6-12 mos). Any suggestions for your wonderful recipes for a substitute for those of us who are not tolerant of coconut?

    • Mickey Trescott says

      Hi Judy! Anytime you see coconut oil, use lard or duck fat instead. If you see coconut milk in a soup recipe, use a thinned root vegetable puree (like parsnip). You’ll want to try dessert recipes specifically developed to be coconut-free instead of adapting those – we have a few in the recipe archives here on the site (check out the pumpkin spice cake!). Good luck!

  • Christin says

    I adore this recipe. First of all, I’m a coconut freak, so that is what made me want to try it out. The way I cook my butter nut squash is to throw it in the crock pot whole, and cook it for about 4 hours on high. This makes cutting the squash so much easier. Just scoop the seeds and junk out later.

    I ended up discarding both skins, and using a small oven proof glass bowl to do the twice baking. I didn’t have any coconut milk, so used some half and half. I also made the mistake of not paying attention to the recipe. My shredded coconut was sweetened, and I folded it in with the rest of the ingredients.

    My husband and daughter loved it, and so did I. They both said that it tasted like Thanksgiving. My husband isn’t a huge fan of squash, so that was a high compliment. Thanks for the recipe. I’ll be making it again.

  • Rose Martine says

    “This was great! Really enjoyed it – thanks for sharing. I do agree with another commenter who said it was a bit sweet – I will definitely reduce the sugar next time (I used regular granulated sugar).

    Can’t wait for leftovers tomorrow! :)”

  • These are so stinkin perfect!! From the picture I assumed you just used jello on each side and it’s nice to see that you did something so much better.

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