These healthy mini blueberry muffins are loaded with whole grains, naturally sweetened and use a secret ingredient: butternut squash!

Originally published on January 30, 2020. Last updated September 20, 2021

Mini wholewheat blueberry muffins on a table with fresh blueberries. One muffin is out of its wrapper.

Homemade muffin recipes are my super power. I love making them, veggie-loading them, and you all seem to dig them just as much (since they are always some of my top recipes). And this particular healthy muffin recipe filled my dreams and many of my waking thoughts this week as I worked to perfect it.

Oy! The dishes! And truthfully, a family of 3 can only eat so many bite-sized muffins. So when I brought these mini whole wheat blueberry muffins to a parent coffee mingle at my daughter’s school, I was beyond dazzled that people were gobbling them up.

The tangy pop of blueberries with the subtle sweetness of butternut squash makes these muffins so delicious! Plus, they are naturally sweetened with bananas and maple syrup, making them the perfect veggie-loaded breakfast for the family to enjoy! Not to mention, they are perfectly sized for easy portioning and fit easily in those little lunch boxes like!

This recipe is….

Vegetarian, nut-free, can easily be dairy-free, naturally sweetened, perfect as part of meal prep, quick to make, and done baking in 15 minutes

Why these mini whole wheat blueberries muffins are amazing!

  • Fluffy and soft. Not overly moist, not too dense.
  • Veggie-loaded with a nice amount of butternut squash.
  • Naturally sweetened with maple syrup or honey and some ripe banana.
  • Quick and easy to make! From start to finish, they are done in under 30 minutes, then they’ll cool for a few minutes after that.
  • Made from whole grains, nut-free and can easily be made dairy-free, by simply using your favorite non-dairy milk.
  • Low mess. They are mixed all in one bowl! Easy peasy.
  • Great for feeding a crowd or for stocking up your freezer since this mini muffin recipe makes about 36 perfectly bite-sized muffins.
Process shot for how to make whole wheat mini blueberry muffins.

Where to find butternut squash puree

I can easily find butternut squash puree in most grocery stores in the following places:

  • with the canned vegetables
  • baking aisle
  • with canned pumpkin in the fall

However, if you can’t find butternut squash puree or just prefer to make your own, you can simple do so by cooking a butternut squash in your preferred way. Drain off any cooking liquid and use a potato masher to mash the fresh or put the cooked butternut squash flesh into a blender and puree!

How do you make blueberry muffins?

  1. Preheat your oven to 350 ℉ and line a mini muffin tin or grease it with extra oil to prevent sticking.
  2. In a large mixing bowl, combine everything except the blueberries. Mix until well combined and batter has a smooth consistency.
  3. Fold in blueberries, saving out a few for topping if desired.
  4. Using a small cookie scoop or heaping tablespoon, portion out the batter into the prepared muffin tins. Top with extra blueberries if desired.
  5. Bake in preheated oven for 12-15 minutes or until a toothpick inserted into he middle of a muffin comes out clean.
  6. Let muffins cool in pan for 5 minutes before transferring to a cooling rack.
  7. Let cool and enjoy! Once completely cool, transfer to a air-tight container and store in fridge for up to 5 days or into freezer for up to a month.

How to store these mini blueberry muffins

I highly suggest storing these mini blueberry muffins in an airtight container in your refrigerator. Because they are so moist, storing them in the refrigerator is your best bet for keeping them fresher longer and prevent molding.

Or, you can freeze these muffins. Since this healthy mini blueberry muffin recipe yields 36 muffins, this is a great recipe to use for stocking up and they freeze really well. I like to store them in a large freezer bag or freezer-safe large container once the muffins have totally cooled.

To defrost, I like to take them out of the freezer and leave them on the counter to thaw overnight. Or if you want one or two NOW, you can warm a muffin in the microwave for about 10 seconds.

Suggested Adaptations

  • Replace the butternut squash puree with sweet potato puree or pumpkin puree in this mini blueberry muffins.
  • Make them gluten free by using gluten-free oat flour in place of the whole wheat flour.
  • Make these whole wheat blueberry muffins as regular size muffins and make them at the same temp for about 25 minutes or until a toothpick inserted into the middle comes out clean.
  • Swap out the blueberries for raisins or chocolate chips!

Other veggie-loaded muffin recipes you need in your life

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Mini wholewheat blueberry muffins on a table with parchment paper, a blue napkin and fresh blueberries.
5 from 12 votes

Mini Whole Wheat Blueberry Muffins (with butternut squash)

Yield: 36 mini muffins
Prep Time: 10 minutes
Cook Time: 15 minutes
Cuisine: American
Course: Breakfast
These healthy mini blueberry muffins are loaded with whole grains, naturally sweetened and use a secret ingredient: butternut squash!

Ingredients
 

  • 3/4 cup butternut squash puree
  • 1/2 cup mashed ripe banana
  • 1/4 cup maple syrup or honey
  • 1/4 cup milk of choice
  • 1 1/2 cups whole wheat flour
  • 1 tsp pumpkin pie spice
  • 1 tsp vanilla extract
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1/3 cup melted coconut oil or avocado oil
  • 2 eggs
  • 1/4 tsp salt
  • 1/4 cup blueberries, (if using frozen, defrost and drain of extra liquid)

Instructions
 

  • Preheat an oven to 350 ℉ and line a mini muffin tin or grease it with extra oil to prevent sticking.
  • In a large mixing bowl, combine everything except the blueberries. Mix until well combined and batter has a smooth consistency.
  • Fold in blueberries, saving out a few for topping if desired.
  • Using a small cookie scoop or heaping tablespoon, portion out the batter into the prepared muffin tins. Top with extra blueberries if desired.
  • Bake in preheated oven for 12-15 minutes or until a toothpick inserted into he middle of a muffin comes out clean.
  • Let muffins cool in pan for 5 minutes before transferring to a cooling rack.
  • Let cool and enjoy! Once completely cool, transfer to an air-tight container and store in fridge for up to 5 days or into freezer for up to a month.
Serving: 1muffin, Calories: 50kcal, Carbohydrates: 6g, Protein: 1g, Fat: 2g, Saturated Fat: 1g, Cholesterol: 9mg, Sodium: 51mg, Potassium: 58mg, Fiber: 1g, Sugar: 2g, Vitamin A: 326IU, Vitamin C: 1mg, Calcium: 14mg, Iron: 1mg