Mini Whole Wheat Blueberry Muffins (with squash)

These healthy mini blueberry muffins are packed with whole grains, naturally sweetened, and sneak in a little surprise ingredient: butternut squash!

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

Baking muffins at home has truly become one of my go-to kitchen wins. I especially love sneaking in veggies whenever I can, and it seems like you all enjoy these little treats just as much as I do—because they’re always some of my most popular recipes. This particular batch of healthy muffins had me dreaming about perfecting them all week long.

Oh, and the cleanup? Yeah, there’s always a mountain of dishes! And honestly, three hungry people can only eat so many bite-sized muffins. So when I took these mini whole wheat blueberry muffins to a school parent coffee event, I was honestly thrilled watching everyone scoop them up happily.

There’s such a lovely balance here—the tart bursts of blueberries paired with the mellow, natural sweetness of butternut squash. Plus, with banana and maple syrup adding sweetness naturally, these muffins make a veggie-packed, kid-friendly morning snack everyone will love. And because they’re bite-sized, they fit perfectly into little lunch boxes, making weekdays easier already!

Vegetarian, nut-free, easily dairy-free, naturally sweetened, great for meal prep, quick to whip up, and ready to eat in just 15 minutes

Looking for a quick, wholesome, and kid-friendly bake that freezes well? You’re in exactly the right spot. These mini whole wheat blueberry muffins sneak in a secret veggie star—sweet butternut squash—that adds moisture and a healthy boost. They’re naturally sweetened with ripe banana and maple syrup, made from simple ingredients you likely have on hand, and sized just right for grab-and-go.

Think soft, fluffy mini muffins bursting with blueberries and wrapped in cozy sweetness from squash and banana. The recipe uses one bowl, takes about 10 minutes to mix, and 12–15 minutes to bake, making about 36 perfectly portioned muffins—ideal for school snacks, breakfasts, or coffee chats with friends. And don’t worry, clean-up won’t keep you late in the kitchen!

• Hands-on time: just about 10 minutes; total bake time: 15 minutes, so you’ll have these muffins done in under 30 minutes.
• Yield: roughly 36 mini muffins.
• Diet-friendly: vegetarian, nut-free, and easily made dairy-free by swapping in your fave plant-based milk.
• Flavor & texture: fluffy, light, naturally sweet, and packed with wholesome veggies.

What Makes Them Special

• Soft and fluffy texture. Not too dense, not overly moist—just right for little hands and big smiles.
• Packed with veggies. That butternut squash adds sneaky nutrition and moisture that keeps these tender. For another veggie-forward bake, try this Carrot Cake Cupcakes Recipe.
• Sweetened naturally. With maple syrup (or honey) plus ripe banana—no processed sugar here!
• Quick and easy. Mix everything in one bowl, get them in the oven, and done in under 30 minutes. For a similarly simple blueberry bake, try these foolproof lemon blueberry scones (step-by-step).
• Whole grain goodness. Made from whole wheat flour, nut-free, and simple to make dairy-free.
• Minimal mess. Just one bowl to wash—total win for busy kitchens.
• Feeds a crowd. Perfect for making a big batch to share or freeze for later. If you’re planning brunch, this Blueberry-Lemon Breakfast Cake also serves a crowd.

Ingredients You’ll Need

• 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)

How to Make Them

1. Preheat oven to 350°F and line a mini muffin pan with paper cups or grease it well with oil.
2. If using frozen blueberries, thaw and drain off any excess liquid.
3. In a large bowl, combine all ingredients except the blueberries and mix until the batter is smooth.

4. Gently fold the blueberries into the batter, reserving a few for topping if desired.

5. Use a small cookie scoop or large tablespoon to fill each mini muffin cup with batter and top with reserved blueberries if using.
6. Bake for 12–15 minutes, or until a toothpick inserted in the center comes out clean.

7. Let muffins rest in the pan about 5 minutes, then transfer to a cooling rack to cool completely.

   

Baker’s Tips for Success

Finding butternut squash puree is easier than you might think. You can usually spot it in a few handy places at the store:

• Near canned veggies
• In the baking aisle
• Among canned pumpkin goods during fall

Can’t find butternut squash puree or prefer the fresh route? No problem! Just cook your butternut squash however you like—roasted, steamed, or boiled—then mash it up with a potato masher or blend it smooth after draining any extra liquid. Fresh puree shines in this recipe!

Mix-Ins and Substitutions

• Swap out butternut squash puree for sweet potato or pumpkin puree. Both bring lovely flavor and moisture.
• Go gluten-free by using gluten-free oat flour instead of whole wheat flour.
• Make regular-sized muffins with this recipe—bake at 350°F for around 25 minutes or until a toothpick comes out clean.
• Mix up the berries! Try raisins or chocolate chips instead of blueberries—or swap in raspberries like these Raspberry Lemon Muffins—for a fun twist.

Mini Whole Wheat Blueberry Muffins (with butternut squash)

Instructions

• Start by preheating your oven to 350 ℉. Grab a mini muffin tin and either line it with paper cups or grease it really well with a little extra oil so your muffins don’t stick.
• In a big bowl, toss everything except the blueberries together. Mix it until the batter is nice and smooth.
• Now gently fold in the blueberries, but hold back a few if you want to sprinkle some on top for extra prettiness.
• Use a small cookie scoop or big tablespoon to fill each muffin cup with batter. If you saved some blueberries for topping, pop those on now!
• Bake for 12-15 minutes, or until a toothpick poked in the center comes out clean.
• Let your muffins rest in the pan for about 5 minutes before moving them to a cooling rack so they finish cooling.
• Once cooled, dig in and enjoy! Store leftovers in an air-tight container in the fridge for up to 5 days or stash in the freezer for up to a month.

Serving: 1 muffin , Calories: 50 kcal , Carbohydrates: 6 g , Protein: 1 g , Fat: 2 g , Saturated Fat: 1 g , Cholesterol: 9 mg , Sodium: 51 mg , Potassium: 58 mg , Fiber: 1 g , Sugar: 2 g , Vitamin A: 326 IU , Vitamin C: 1 mg , Calcium: 14 mg , Iron: 1 mg

Just a heads up: the nutrition info here is an estimate to give you a general idea. It can change depending on the exact ingredients or brands you use.

How to Store and Freeze

To keep these mini blueberry muffins fresh and delicious, I recommend storing them in an airtight container in your fridge. Because they’re nice and moist, refrigeration helps prevent them from molding and keeps them tasting fresh longer. This same approach works for other muffins—try it with lemon poppy seed muffins or rhubarb muffins too.

You can also freeze these muffins to have on hand for busy mornings. Since this recipe makes a big batch of about 36 muffins, it’s perfect for stocking your freezer. Once completely cool, pop them into a big freezer bag or container that seals tight.

When you’re ready to enjoy, just thaw overnight on your countertop. If you’re in a hurry and want a warm muffin, zap it in the microwave for about 10 seconds and you’re good to go.

Questions You Might Have

Are these muffins dairy-free? Absolutely! Just pick your favorite non-dairy milk, and since the recipe uses melted coconut or avocado oil, you don’t need any dairy at all.

Can I use honey instead of maple syrup? Yes! Maple syrup or honey both work beautifully here—just use what you have on hand or prefer.

Can I use frozen blueberries? Sure! Just be sure to thaw them first and drain off any extra liquid so your muffins don’t get soggy.

What if I don’t have butternut squash puree? Swap in sweet potato or pumpkin puree, or make your own by cooking and mashing fresh butternut squash. Drain any liquid to keep the batter consistency right.

How should I store and reheat leftovers? Once cooled, keep muffins in an airtight container in the fridge for up to 5 days or freeze for up to a month. Thaw on the counter overnight or microwave a single muffin for 10 seconds when in a rush.

Can I make these as full-size muffins? Definitely! Bake at the same 350°F temperature for roughly 25 minutes. Check with a toothpick for doneness. For another full-size fruit muffin recipe, try these Strawberry-Rhubarb Muffins.

Is there a gluten-free version? Yes! Simply use gluten-free oat flour instead of whole wheat flour.

How many muffins does this recipe make? You’ll get about 36 cute mini muffins from this recipe.

Are these muffins nut-free and school safe? Yes, this recipe contains no nuts, making it a friendly option for school lunches—just be sure to double-check your school’s allergy policies.

What about egg-free or vegan options? The basic recipe calls for two eggs. If you need to avoid eggs, you can try flax eggs or a commercial egg replacer, but keep in mind texture might change slightly, and you may have to adjust bake times or liquids. If you’d prefer a fully plant-based dessert without substitutions, try our Vegan Rhubarb Crumble (gluten-free).