These Healthy Pumpkin Muffins are a delightful blend of cozy flavors and wholesome ingredients, perfect for any time of day. With a moist, tender crumb and a hint of warm spices, each bite feels like a comforting hug. The natural sweetness of pumpkin pairs beautifully with a subtle nuttiness, making them both satisfying and guilt-free. Ready in just 35 minutes, they’re an easy treat to whip up for breakfast, snacks, or even dessert.
What makes these muffins truly special is their irresistible texture—soft, fluffy, and lightly spiced with cinnamon and nutmeg. They’re packed with nutrients, yet taste indulgent enough to feel like a treat. Whether you’re enjoying them fresh out of the oven or savoring them later, these muffins are sure to brighten your day. Plus, they’re a great way to sneak in some extra veggies without compromising on flavor!
Ingredients for Healthy Pumpkin Muffins

- 1 cup pumpkin puree (canned or homemade)
- 2 large eggs
- ⅔ cup milk (dairy or non-dairy alternatives like almond or oat milk)
- ⅓ cup melted coconut oil or vegetable oil
- ⅓ cup maple syrup (or honey as a substitute)
- 1 tablespoon apple cider vinegar
- 1 teaspoon vanilla extract
- 1 cup all-purpose flour, spooned and leveled
- ¾ cup whole wheat flour, spooned and leveled
- 1 tablespoon pumpkin pie spice (or make your own with cinnamon, nutmeg, ginger, and cloves)
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon sea salt
Step-by-Step Instructions
- Preheat the oven to 350°F and lightly grease or spray a 12-cup muffin tin.
- In a large bowl, combine the pumpkin puree, eggs, milk, oil, maple syrup, vinegar, and vanilla. Whisk until smooth and well combined.
- In a medium bowl, whisk together the all-purpose flour, whole wheat flour, pumpkin pie spice, baking powder, baking soda, and salt.
- Add the dry ingredients to the wet ingredients and stir until just combined. Avoid overmixing to keep the muffins tender.
- Use a ⅓-cup measuring scoop to divide the batter evenly into the prepared muffin tin.
- Bake for 18 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
- Let the muffins cool in the pan for 10 minutes, then transfer them to a wire rack to cool completely.
Delicious Toppings to Elevate Your Muffins
Add a little extra flair to your Healthy Pumpkin Muffins with these tasty toppings! Try a dollop of whipped cream cheese or a drizzle of honey for a sweet and tangy twist. For a crunchy finish, sprinkle chopped pecans or pumpkin seeds on top before baking. If you’re feeling indulgent, a light dusting of powdered sugar or a smear of almond butter works wonders.
How to Store and Keep Them Fresh?
These muffins stay fresh for up to 3 days when stored in an airtight container at room temperature. For longer storage, wrap them individually in plastic wrap and freeze for up to 3 months. To reheat, simply pop them in the microwave for 15-20 seconds or warm them in a 300°F oven for 5-10 minutes for that fresh-baked taste.
Easy Swaps for Dietary Needs
Make these muffins work for your diet with a few simple swaps! Use almond or oat milk instead of regular milk for a dairy-free version. Swap the maple syrup for honey or a sugar-free alternative if preferred. For a gluten-free option, replace the flours with a 1:1 gluten-free baking blend. These tweaks keep the recipe versatile and inclusive.
Perfect Pairings for Serving
Enjoy these muffins as part of a cozy breakfast or snack. Pair them with a hot cup of coffee, chai tea, or a glass of cold almond milk for a comforting treat. They also make a great addition to a brunch spread alongside fresh fruit, yogurt, or a savory egg dish. Perfect for any time of day!

Healthy Pumpkin Muffins
Ingredients
- 1 cup pumpkin puree
- 2 large eggs
- ⅔ cup milk
- ⅓ cup melted coconut oil or vegetable oil
- ⅓ cup maple syrup
- 1 tablespoon apple cider vinegar
- 1 teaspoon vanilla extract
- 1 cup all-purpose flour, spooned and leveled
- ¾ cup whole wheat flour, spooned and leveled
- 1 tablespoon pumpkin pie spice
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon sea salt
Instructions
- Preheat the oven to 350°F and lightly grease or spray a 12-cup muffin tin.
- In a large bowl, combine the pumpkin puree, eggs, milk, oil, maple syrup, vinegar, and vanilla and whisk until combined.
- In a medium bowl, whisk together the flours, pumpkin pie spice, baking powder, baking soda, and salt.
- Add the dry ingredients to the wet ingredients and stir until just combined.
- Use a ⅓-cup measuring scoop to divide the batter into the muffin tin. Bake for 18 to 20 minutes, or until a toothpick inserted comes out clean.
- Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely.