Irresistible Butternut Squash Muffins

I didn’t try butternut squash until I was in my twenties. Growing up, my mom stuck to regular vegetables like carrots and green beans. Squash seemed too fancy and complicated.

Turns out I was totally wrong. Butternut squash is actually pretty easy to work with, and it makes amazing muffins. The squash adds natural sweetness and keeps them moist without being heavy. Plus, you can sneak some extra nutrition into breakfast without anyone complaining.

What Kind of Butternut Squash Should I Use?

Any butternut squash from the grocery store will work perfectly for these muffins, but you’ll want to pick one that feels heavy for its size and has a firm, tan-colored skin without soft spots. A small butternut squash typically weighs around 2-3 pounds, which should give you plenty of cooked squash for this recipe with some leftover. You can roast the squash yourself by cutting it in half, scooping out the seeds, and baking it cut-side down at 400°F until tender, or save time by using pre-cut butternut squash from the produce section. Just make sure to cook it until it’s soft enough to mash easily, and let it cool completely before adding it to your muffin batter.

Options for Substitutions

These muffins are pretty forgiving when it comes to swaps, so here are some options if you need to make changes:

• Butternut squash: You can easily substitute with canned pumpkin puree (about 1 ½ cups) or even sweet potato puree. If using fresh sweet potato, roast it the same way you would the squash.
• Whole wheat flour: If you don’t have whole wheat flour, just use 3 cups of all-purpose flour total. The muffins will be a bit lighter in texture but still tasty.
• Vegetable oil: You can swap this with melted butter, coconut oil, or even applesauce for a lighter option. If using applesauce, start with ⅓ cup and add more if the batter seems too thick.
• Brown sugar: White sugar works fine if that’s all you have, or try maple syrup (reduce other liquids by 2 tablespoons) for a nice fall flavor.
• Spices: Don’t stress if you’re missing one or two spices. The cinnamon and nutmeg are the most important ones. You can also just use 2 teaspoons of pumpkin pie spice instead of the individual spices.
• Raisins and walnuts: Feel free to swap raisins with dried cranberries or chopped dates, and replace walnuts with pecans or pumpkin seeds. You can also leave them out completely if you prefer plain muffins.

Watch Out for These Mistakes While Baking

The biggest mistake when making butternut squash muffins is using undercooked or watery squash, which can make your muffins dense and soggy – make sure to roast the squash until it’s completely tender and let any excess moisture evaporate before mashing.

Overmixing the batter is another common error that leads to tough, chewy muffins, so gently fold the wet and dry ingredients together just until combined, even if the batter looks a bit lumpy.

Don’t skip the step of tossing your raisins and walnuts in a little flour before adding them to the batter, as this prevents them from sinking to the bottom during baking.

Finally, resist the urge to overbake – test with a toothpick inserted in the center, and remove the muffins when it comes out with just a few moist crumbs, as they’ll continue cooking slightly in the hot pan.

What to Serve With Butternut Squash Muffins?

These spiced butternut squash muffins are perfect for breakfast or an afternoon snack with a hot cup of coffee or chai tea. I love spreading a little butter or cream cheese on them while they’re still warm – the creamy texture pairs beautifully with all those cozy fall spices. They also make a great addition to a brunch spread alongside scrambled eggs and fresh fruit, or you can pack them for an easy grab-and-go breakfast with some Greek yogurt on the side. For a special treat, try drizzling them with a simple maple glaze or serving them with a dollop of whipped cream.

Storage Instructions

Keep Fresh: These butternut squash muffins stay moist and delicious when stored in an airtight container at room temperature for up to 3 days. If you want them to last a bit longer, pop them in the fridge where they’ll keep for up to a week – just let them come to room temperature before eating for the best texture.

Freeze: I love making a double batch of these muffins because they freeze so well! Wrap each muffin individually in plastic wrap or store them in a freezer-safe container for up to 3 months. They’re perfect for grabbing a quick breakfast or snack straight from the freezer.

Thaw: To enjoy your frozen muffins, just let them thaw at room temperature for about 30 minutes, or pop them in the microwave for 20-30 seconds. You can also warm them up in a 350°F oven for 5-10 minutes if you prefer them toasty and fresh-tasting.

Preparation Time	20-30 minutes
Cooking Time	15-20 minutes
Total Time	35-50 minutes
Level of Difficulty	Medium

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 3100-3400
• Protein: 50-60 g
• Fat: 110-125 g
• Carbohydrates: 480-520 g

Ingredients

For the squash mixture:

• 3 eggs (room temperature)
• 1/2 cup brown sugar (packed)
• 1/2 cup neutral oil (I use canola)
• 1 small butternut squash (about 2 lbs, roasted and pureed)
• 1/2 cup water
• 1/2 cup sugar

For the dry blend:

• 1 1/2 tsp ground cinnamon (freshly ground preferred)
• 1 1/2 tsp baking soda
• 1 cup all-purpose flour (I use King Arthur)
• 1/2 tsp ground cloves
• 1/2 tsp pumpkin pie spice
• 1/2 tsp salt
• 2 cups whole wheat flour
• 1/4 cup raisins (plumped in warm water, optional but adds moisture)
• 1/4 cup walnuts (chopped into 1/4-inch pieces)
• 1/2 tsp ground nutmeg
• 1 1/2 tsp baking powder

Step 1: Prepare the Butternut Squash and Preheat the Oven

• 1 small butternut squash

Start by preheating your oven to 400°F and greasing 20 muffin cups with a light coating of oil or cooking spray.

While the oven heats, prepare the butternut squash by carefully cutting a small hole in the top with a sharp knife—this allows steam to escape safely.

Microwave the whole squash for 9-12 minutes until the flesh is completely soft when pierced with a fork.

Remove from the microwave and let it cool for about 20 minutes until you can handle it comfortably.

Once cooled, carefully halve the squash and scoop out all the seeds with a sturdy spoon, then measure out 1 1/2 cups of the roasted squash puree for your batter.

Step 2: Create the Wet Ingredient Base

• 3 eggs
• 1/2 cup water
• 1/2 cup neutral oil
• 1/2 cup sugar
• 1/2 cup brown sugar

In a large mixing bowl, combine the 1 1/2 cups of butternut squash puree with the room temperature eggs, water, neutral oil, and both sugars.

Whisk these ingredients together thoroughly until the mixture is smooth and well-combined—this is crucial for even moisture distribution throughout your muffins.

The room temperature eggs are important here because they incorporate more smoothly into the wet mixture, creating a better emulsion.

I like to use a whisk rather than a spoon for this step to ensure the sugars dissolve completely and you get a uniform batter with no lumps of squash remaining.

Step 3: Combine Dry Ingredients and Spice Mixture

• 2 cups whole wheat flour
• 1 cup all-purpose flour
• 1 1/2 tsp baking powder
• 1 1/2 tsp baking soda
• 1/2 tsp salt
• 1 1/2 tsp ground cinnamon
• 1/2 tsp ground nutmeg
• 1/2 tsp ground cloves
• 1/2 tsp pumpkin pie spice

In a separate medium bowl, whisk together the whole wheat flour, all-purpose flour, baking powder, baking soda, salt, and all spices (cinnamon, nutmeg, cloves, and pumpkin pie spice).

Whisking these dry ingredients together ensures the leavening agents and spices are evenly distributed throughout the flour, which prevents pockets of dense batter or uneven flavor.

I prefer to freshly grind my cinnamon when possible—it makes a noticeable difference in the final flavor, giving the muffins a warmer, more authentic spice profile than pre-ground.

Step 4: Build the Complete Batter

• dry ingredient mixture from Step 3
• wet ingredient mixture from Step 2
• 1/4 cup raisins
• 1/4 cup walnuts

Pour the dry ingredient mixture from Step 3 into the wet ingredient base from Step 2 and fold them together gently using a spatula or wooden spoon, stirring just until the dry ingredients are completely moistened and no flour streaks remain.

Don’t overmix—muffin batter should be slightly lumpy as overmixing develops gluten and results in tough, dense muffins.

Once the flour is incorporated, fold in the plumped raisins (if using) and chopped walnuts, distributing them evenly throughout the batter so every muffin gets some texture and flavor.

Step 5: Fill, Bake, and Cool the Muffins

Spoon the batter evenly into the prepared muffin cups, filling each cup about three-quarters full to allow room for the muffins to rise during baking.

Place the muffin pan in your preheated 400°F oven and bake for 15 minutes until the tops are golden brown and a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs.

Remove from the oven and let the muffins cool in the pan for 10 minutes—this allows them to set and makes them easier to remove without crumbling.

After 10 minutes, gently turn the muffins out onto a wire cooling rack to cool completely before serving.