Fluffy Vegan Butternut Squash Muffins

Fall baking season is when I really come alive in the kitchen. There’s something about the smell of cinnamon and nutmeg that makes me want to pull out every baking dish I own. But I’ll be honest – I used to skip right past butternut squash recipes because they seemed like too much work.

That’s before I discovered how easy it is to roast squash ahead of time. Now I’ll roast a whole squash on Sunday and use it throughout the week. These muffins are perfect for using up that roasted squash, and they’re completely vegan without tasting like they’re missing anything.

The best part? My kids actually ask for these. They love the soft texture and warm spices, and I love that they’re getting vegetables for breakfast. Win-win in my book.

What Kind of Butternut Squash Should I Use?

For these muffins, you’ll want to use pureed butternut squash, which you can either make yourself or buy pre-made from the store. If you’re making it from scratch, look for a butternut squash that feels heavy for its size and has a smooth, tan-colored skin without any soft spots. You can roast it in the oven until tender, then scoop out the flesh and puree it until smooth. Store-bought butternut squash puree works just as well and saves you time – just make sure it’s plain puree without any added spices or sweeteners. The recipe also mentions that pumpkin puree can be substituted if that’s what you have on hand, so don’t worry if butternut squash isn’t available.

Options for Substitutions

These vegan muffins are pretty adaptable, so here are some swaps you can make:

• Whole-wheat pastry flour: If you can’t find whole-wheat pastry flour, the recipe already gives you a great substitute – just mix 1 1/2 cups whole wheat flour with 1 cup all-purpose flour. You can also use all-purpose flour for lighter muffins or try oat flour for a nuttier taste.
• Butternut squash puree: Pumpkin puree works perfectly as mentioned, but you can also try sweet potato puree or even mashed banana for a different flavor profile. Just keep the same amount.
• Tofu and nondairy milk mixture: This acts as an egg replacer, so you can substitute with 2 flax eggs (2 tbsp ground flax mixed with 6 tbsp water, let sit for 5 minutes) or use 1/2 cup applesauce instead.
• Almond milk: Any nondairy milk works here – oat milk, soy milk, or coconut milk will all do the trick. Even regular milk if you’re not strictly vegan.
• Avocado oil: Swap with any neutral oil like vegetable or canola oil. You can also use melted coconut oil, just make sure it’s cooled slightly before mixing.
• Flaxmeal: Chia seeds ground up work well, or you can simply omit this if you don’t have either – it adds nutrition but isn’t essential for the muffin structure.

Watch Out for These Mistakes While Baking

The biggest mistake when making vegan muffins is overmixing the batter, which can lead to tough, dense muffins instead of light and fluffy ones – mix just until the ingredients are combined and you still see a few lumps.

Another common error is not blending the tofu mixture completely smooth, so make sure to blend it with the nondairy milk until it’s creamy with no chunks, otherwise you’ll end up with an uneven texture.

Don’t skip letting the flaxmeal sit for a few minutes after mixing it with a tablespoon of water to create a gel-like consistency, as this acts as your egg replacement and helps bind everything together.

Finally, resist the urge to open the oven door too early – vegan baked goods can be more delicate and need that consistent heat to rise properly, so wait until at least 18-20 minutes before checking for doneness with a toothpick.

What to Serve With Vegan Butternut Squash Muffins?

These muffins are perfect for breakfast or an afternoon snack, and they pair beautifully with a hot cup of coffee or chai tea to complement those warm, cozy flavors. I love serving them alongside a bowl of oatmeal or yogurt (use coconut or almond yogurt to keep it vegan) for a more filling breakfast. They also make a great addition to a fall brunch spread with some fresh fruit like sliced apples or pears. For an extra treat, try spreading a little almond butter or vegan cream cheese on top – the creamy texture goes perfectly with the soft, spiced muffin.

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. I like to line the container with a paper towel to absorb any extra moisture. If your kitchen is really warm, pop them in the fridge where they’ll keep for up to a week.

Freeze: Muffins are perfect for freezing! Wrap each one individually in plastic wrap or store them in a freezer bag with parchment paper between layers. They’ll stay fresh in the freezer for up to 3 months, making them great for quick breakfast grab-and-go options.

Thaw: To enjoy frozen muffins, just leave them on the counter for about 30 minutes to thaw completely. If you’re in a hurry, you can microwave them for 20-30 seconds on medium power. They taste just as good as fresh, and the butternut squash keeps them nice and moist even after freezing.

Estimated Nutrition

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

• Calories: 1800-2000
• Protein: 34-38 g
• Fat: 32-36 g
• Carbohydrates: 362-380 g

Ingredients

For the dry mixture:

• 2 1/2 cups whole-wheat pastry flour (or 1 1/2 cups whole wheat flour plus 1 cup all-purpose flour as an alternative)
• 2 tsp baking powder
• 1/2 tsp baking soda
• 1/4 tsp salt
• 2 tbsp ground flaxseed

For the wet mixture:

• 3/4 cup pureed butternut squash or pumpkin
• 1/2 cup extra-firm tofu blended with 1/4 cup nondairy milk
• 1/4 cup almond or other nondairy milk
• 1 tbsp avocado oil or neutral oil

For sweetness:

• 1 cup granulated sugar

Step 1: Blend the Tofu and Milk

• 1/2 cup extra-firm tofu blended with 1/4 cup nondairy milk

In a blender or food processor, combine the extra-firm tofu with 1/4 cup of nondairy milk.

Blend until completely smooth and creamy.

Set aside for later use.

Step 2: Mix the Dry Ingredients

• 2 1/2 cups whole-wheat pastry flour (or 1 1/2 cups whole wheat flour plus 1 cup all-purpose flour as an alternative)
• 2 tsp baking powder
• 1/2 tsp baking soda
• 1/4 tsp salt

In a large mixing bowl, whisk together the whole-wheat pastry flour (or your chosen flour combination), baking powder, baking soda, and salt until well combined.

This ensures the leaveners are evenly distributed, giving the muffins an even rise.

Step 3: Prepare the Wet Ingredients

• 3/4 cup pureed butternut squash or pumpkin
• blended tofu mixture from Step 1
• 2 tbsp ground flaxseed
• 1 tbsp avocado oil or neutral oil
• 1 cup granulated sugar

In a separate bowl, mix together the pureed butternut squash or pumpkin, the blended tofu mixture from Step 1, ground flaxseed, oil, and granulated sugar.

Stir until everything is well combined and the sugar has mostly dissolved.

I always find that letting the mixture sit for a minute allows the flaxseed to start absorbing moisture, which helps the muffins hold together better.

Step 4: Combine Wet and Dry Ingredients

• wet ingredients from Step 3
• dry ingredients from Step 2
• 1/4 cup almond or other nondairy milk

Pour the wet mixture from Step 3 into the bowl with the dry ingredients from Step 2.

Gently stir until just combined—be careful not to overmix.

It’s perfectly fine if you see a few small lumps.

Overmixing can make the muffins tough instead of tender.

If the batter seems too thick, add the remaining 1/4 cup of nondairy milk as needed.

Step 5: Prepare the Muffin Pan and Bake

Preheat the oven to 375°F (190°C).

Spray a muffin pan with oil or line it with paper liners.

Evenly scoop the batter into the prepared pan.

For large muffins, use a 6-cup pan; for standard size muffins, use a 12-cup pan.

Bake for 15 minutes if using standard pans, or 18–19 minutes for large muffins.

To test doneness, insert a toothpick into the center of a muffin—it should come out dry or with a few crumbs.

If not, bake for another couple of minutes and check again.

I like to rotate the pan halfway through baking to ensure even cooking.

Step 6: Cool and Serve

Allow the baked muffins to cool in the pan on a rack for 10 minutes.

Then carefully remove the muffins from the pan and place them directly on the wire rack to cool completely.

Enjoy your freshly baked, wholesome muffins!

For extra flavor, I sometimes serve these with a dab of vegan butter or a drizzle of maple syrup.

Fluffy Vegan Butternut Squash Muffins

Delicious Fluffy Vegan Butternut Squash Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 12 minutes mins

Cook Time 25 minutes mins

Total Time 37 minutes mins

Servings 4

Calories 1900 kcal

Ingredients

  

For the dry mixture:

• 2 1/2 cups whole-wheat pastry flour (or 1 1/2 cups whole wheat flour plus 1 cup all-purpose flour as an alternative)
• 2 tsp baking powder
• 1/2 tsp baking soda
• 1/4 tsp salt
• 2 tbsp ground flaxseed

For the wet mixture:

• 3/4 cup pureed butternut squash or pumpkin
• 1/2 cup extra-firm tofu blended with 1/4 cup nondairy milk
• 1/4 cup almond or other nondairy milk
• 1 tbsp avocado oil or neutral oil

For sweetness:

• 1 cup granulated sugar

Instructions

 

• In a blender or food processor, combine the extra-firm tofu with 1/4 cup of nondairy milk. Blend until completely smooth and creamy. Set aside for later use.
• In a large mixing bowl, whisk together the whole-wheat pastry flour (or your chosen flour combination), baking powder, baking soda, and salt until well combined. This ensures the leaveners are evenly distributed, giving the muffins an even rise.
• In a separate bowl, mix together the pureed butternut squash or pumpkin, the blended tofu mixture from Step 1, ground flaxseed, oil, and granulated sugar. Stir until everything is well combined and the sugar has mostly dissolved. I always find that letting the mixture sit for a minute allows the flaxseed to start absorbing moisture, which helps the muffins hold together better.
• Pour the wet mixture from Step 3 into the bowl with the dry ingredients from Step 2. Gently stir until just combined—be careful not to overmix. It's perfectly fine if you see a few small lumps. Overmixing can make the muffins tough instead of tender. If the batter seems too thick, add the remaining 1/4 cup of nondairy milk as needed.
• Preheat the oven to 375°F (190°C). Spray a muffin pan with oil or line it with paper liners. Evenly scoop the batter into the prepared pan. For large muffins, use a 6-cup pan; for standard size muffins, use a 12-cup pan. Bake for 15 minutes if using standard pans, or 18–19 minutes for large muffins. To test doneness, insert a toothpick into the center of a muffin—it should come out dry or with a few crumbs. If not, bake for another couple of minutes and check again. I like to rotate the pan halfway through baking to ensure even cooking.
• Allow the baked muffins to cool in the pan on a rack for 10 minutes. Then carefully remove the muffins from the pan and place them directly on the wire rack to cool completely. Enjoy your freshly baked, wholesome muffins! For extra flavor, I sometimes serve these with a dab of vegan butter or a drizzle of maple syrup.