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    Home » Recipes » Muffins and Breads

    Butternut Squash Muffins with Apples and Cinnamon

    By Marjory Pilley Published Sep 23, 2019 · Updated Nov 19, 2021

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    This post may contain affiliate links. Please read my disclosure.

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    Plate of butternut squash muffin with cinnamon and apples

    Butternut Squash Muffins with apples, cinnamon, and walnuts are packed with protein since they use Greek yogurt instead of oil. Enjoy them for a healthy snack or even breakfast.

    Healthy butternut squash muffins with apple stacked on a plate.

    So...why would you want to make Butternut Squash Muffins when there are so many fantastic pumpkin muffin recipes out there? I'm so glad you asked! Here's why:

    1. You've finally realized how easy it is to make crock-pot butternut squash puree and now you have lots of it to use up.
    2. You're not a pumpkin fanatic but still want to enjoy a delicious fall-inspired muffin.
    3. You've eaten way too many healthy chocolate pumpkin muffins lately and need a change.
    4. You need a veggie-loaded, protein-packed snack to curb your mid-day slump.
    5. They look delicious. (They are!)

    These are all reasons why we can't get enough of these tasty little muffins, except for #2. You won't find any pumpkin protestors at my house.

    This recipe is a variation of Healthy Pumpkin Muffins with Chocolate Chips and is part of our collection of healthy Greek yogurt muffins!

    Butternut squash apple muffins on a serving board.

    How to Make Butternut Squash Puree

    You'll need about 1 ½ cups of butternut squash puree for this recipe. And, there are a couple of ways to get started.

    1. Cook butternut squash using one of these methods:
      • Make it in a slow cooker. Place the whole butternut squash in a crock-pot and cook on high for 3-4 hours or on low for 4-6 hours. This is our preferred method!
      • Roast it. Cut squash in half lengthwise. Remove seeds and place face down on a baking sheet. Bake in a 375 degree F oven for about 40 minutes or until fork-tender.
      • Bake or microwave butternut squash cubes. You can usually find fresh or frozen cubes at most grocery stores.
    2. Use a fork to mash cooked butternut squash into a uniform consistency. The result does not need to be perfectly smooth. But, if you want perfection, give it a whirl in a food processor.
    3. Place the puree in a strainer to remove excess liquid, if necessary, before measuring out what you'll need for the recipe.

    Note: Check the label for frozen butternut squash carefully to make sure it is not mixed with other ingredients and/or seasoned.

    By the way, if you have extra butternut squash puree, make soup like this Spicy Butternut Squash Soup or simply add butter and seasoning and enjoy!

    Crock-pot butternut squash in a bowl in front of a slow cooker

    Tips for Adding Apples to Butternut Squash Muffins

    Apples give these muffins extra sweetness and add a little extra moisture.

    • Opt for a sweet apple such as Honey Crisp, Royal Gala, Fuji or Ambrosia.
    • You can, but you do not have to peel the apple first. I add cubes with skin to the batter.
    • If the apple is sweet enough, you MAY be able to opt for a little less sugar!

    Be sure and watch the video to see the making of this butternut squash muffin recipe in action!

    Hand holding butternut squash apple muffin with bite removed.

    More Healthy Muffins

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      Healthy Oatmeal Pumpkin Muffins or "Cups" {Gluten-free}
    • Two spaghetti squash muffins au gratin on a plate with more on a platter behind them.
      Spaghetti Squash Muffins (Au Gratin Cups)
    • Healthy Banana Muffin Recipe with Greek Yogurt
      Healthy Banana Muffins with Greek Yogurt

    Did you make this recipe?
    Please leave a rating and tell us how you liked it!

    📋 Recipe

    Butternut squash muffins with apple stacked on a plate.

    Butternut Squash Muffins with Apples

    Butternut Squash Muffins with apples, cinnamon, and walnuts are packed with protein since they use Greek yogurt instead of oil. Enjoy them for a healthy snack or even breakfast.
    5 from 2 votes
    Email Ingredients + Recipe
    Print Pin Rate
    Course: Snack
    Cuisine: American
    Prep Time: 10 minutes minutes
    Cook Time: 25 minutes minutes
    Total Time: 35 minutes minutes
    Servings: 12 muffins
    Calories: 139kcal
    Author: Marjory Pilley

    Ingredients

    • 1 ½ cup white whole wheat flour or whole wheat pastry flour
    • ½ cup sugar
    • ½ teaspoon baking powder
    • ½ teaspoon baking soda
    • ½ teaspoon salt
    • ½ teaspoon ground cinnamon
    • 1 ½ cups butternut squash puree
    • 1 egg beaten
    • 5.3 ounce non-fat Greek yogurt
    • ½ cup apple diced
    • ½ cup walnuts chopped

    Instructions

    • Preheat oven to 350 °F.
    • Combine flour, sugar, baking powder, baking soda, salt and cinnamon in a bowl.
    • Stir butternut squash, egg and yogurt into the dry mix.
    • Fold diced apple and chopped walnuts into the batter.
    • Fill muffins tins coated with cooking spray about ⅔ full. (Tip: if using liners, give them a light spritz of cooking spray before filling with batter.)
    • Bake for 20-25 minute or until the muffins are firm and lightly browned on the top.
    • Allow muffins to cool for 5 minutes and then remove to a wire rack to cool further.
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    Nutrition

    Calories: 139kcal | Carbohydrates: 23g | Protein: 5g | Fat: 4g | Saturated Fat: 1g | Cholesterol: 14mg | Sodium: 154mg | Potassium: 183mg | Fiber: 2g | Sugar: 10g | Vitamin A: 1880IU | Vitamin C: 4mg | Calcium: 41mg | Iron: 1mg
    Nutritional and Food Safety Disclaimer

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      Recipe Rating




    1. Jessica Formicola

      September 23, 2019 at 7:47 pm

      5 stars
      I love finding new ways to incorporate veggies into recipes, and these muffins are perfect! I can't wait to try them!

      Reply
    2. Claudia

      September 23, 2019 at 7:52 pm

      5 stars
      I love butternut squash and would be happy to take the whole batch off your hands before I make them:) these look yummy

      Reply

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    Plate of butternut squash muffin with cinnamon and apples

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