Shepherd’s Pie with Mashed Butternut Squash (Paleo and GAPS friendly)

My son loves this version of Shepherd’s Pie with mashed butternut squash.  Whenever I make it, he seems to gobble it up (impressive but not great on his digestion I guess!)  I also love making Shepherd’s Pie GAPS-friendly by using mashed cauliflower.  However, the butternut squash is sweeter and goes great with the meat filling.  You can call it simple comfort food.  Enjoy!

Recipe for Shepherd’s Pie with Mashed Butternut Squash (dairy-free, gluten-free, nightshade-free, GAPS and Paleo friendly)

  • 1 1/2 pounds butternut squash
  • 3 tablespoons coconut oil
  • 1/2 onion, diced
  • 2 carrots, diced
  • 1 pound ground beef or ground turkey
  • 1 teaspoon dried thyme
  • 1/2 teaspoon sea salt
  • 1/4 teaspoon black pepper
  • 1/2 cup frozen peas


1. Peel and seed the squash.  Cut into large cubes and then steam the squash in a large pot over medium heat for about 20 minutes, or until cooked through and very soft.

2. While the squash is cooking, heat 1 Tbsp. coconut oil over medium heat in a large cast iron skillet. Sauté onions in skillet until tender over medium heat, about 10 minutes. Add the carrots and cook for another 5-8 minutes until soft.

3. Add ground beef or turkey and sauté until no longer pink, breaking it up with a spoon as it cooks. Add salt, pepper, thyme and peas.  Cook another 5 or so minutes to cook the peas.

4. Drain the squash and place into a food processor. Add 2-4 Tbsp. coconut oil or butter, salt and pepper to taste and process until smooth.  (You can also use a stick blender in the pot if you have one, or simply a potato masher.)

5. Place beef and onion mixture in 9 x 12 baking dish. Distribute mashed butternut squash on top.  Heat in oven at 375 F if necessary to warm up, otherwise serve as is.

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  1. Sarah, I never thought to use butternut squash with my Shepherd’s pie! What a great idea! Thanks!

  2. Hi Debbie,
    I am not sure where I got the idea but I don’t think it originated in my brain. I did come up with this recipe but really can’t remember where the seed was planted. enjoy!

  3. Heather Brandt says:

    I didn’t think green peas were GAPS friendly.

  4. Hi Heather,
    Yes, both split and green peas are legal. You can find it listed on the allowed food list at http://www.GAPSdiet.com. enjoy!

  5. Hi can someone help me find recipes suitable for a Candida diet? They need to be sugar free (all forms no starches no honey etc) and gluten free. I’m having a hard time finding things to make.

  6. Hi Myra,
    These may be more limited than you would like but they are great for anti-candida – https://allergyfreemenuplanners.com/our-menu-planners/allergy-free-menu-planners/elimination-and-detox-weekly-menu-planner/ You can get the first menu planner here. If you want more menus, I have 4 more of this diet on the membership site.

  7. I’m not even sure how I tripped into this site and recipe, I was clicking around links on some other site, I am sure, lol. But – thanks so much for posting this!!! I adore Shepherd’s Pie and miss it a lot since going low carb/grain-free/mostly Paleo. Other than the mashed cauliflower routine that lots of folks use to sub for potatoes, I had not even thought of this. I will try it!!!

  8. Do you think this could be made ahead and frozen? Would I just do all the steps up until heating at 375, leaving that part for once it comes out of the freezer?

  9. Hi Tara,
    Yes that would work great. You may want to freeze it in the dish you plan on baking it in. Or you could freeze the cooked squash and meat filling separately, defrost, then assemble in the pan. Enjoy!

  10. I’m wanting to prepare these things ahead of time, prior to the arrival of a baby…so I’m concerned about having enough dishes to freeze them in. I saw an idea to freeze things in the dish (though the ones I saw were more like 8×8 or 9×9 square dish, not 9×13) with a liner of parchment paper, then remove the food/parchment once frozen and store in a freezer bag. But that would only work with a square, not a 9×13 rectangle, I suppose. I’d prefer to avoid the aluminum disposable ones. Any other ideas for how to freeze things in bulk without needing lots of dishes stacked in the freezer?

  11. What I would do is get a bunch of tupperware containers and freeze smaller portions of this and other freezeable items. Find containers that are about 2-3 cups, you can use plastic or glass depending upon your budget. Then make mini casseroles in each one, putting the meat on the bottom and the squash on top. This would serve 1-2 people and it won’t take up as much space. They also stack well in the freezer. This is how I package the food I make for my clients. good luck with the new babe!

  12. Good idea! But just to clarify… are you saying to bake the whole casserole and then prepare these smaller portions, or to freeze the smaller portions and then put them in a baking dish and put in the oven later when needed?

  13. I would simply make the meat and the squash separately, then make the layers (like mini casseroles) in the containers without baking it first. If you use glass, you can bake it in the container once defrosted or just transfer it to a baking dish to heat up.

  14. Hi, Sara

    Saturday rainy afternoon here in South Africa, wondering what to make for dinner.. And there was your recipe.

    Thanks so much, comfort food indeed.


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