These healthy pumpkin muffins are moist, fluffy and filled with warm pumpkin spice flavor. They’re made with whole wheat flour, a touch of brown sugar and heart-healthy olive oil for a wholesome fall treat you’ll want on repeat.
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The Muffins I Can’t Stop Making This Fall
Fall is hands down my favorite season for baking. From pumpkin bars and pumpkin banana bread (IYKYK) to apple everything, I’m here for it all. But these healthy pumpkin muffins are the ones I keep coming back to. They’re moist, fluffy, and packed with warm pumpkin spice flavor, yet secretly loaded with whole grains and healthy fats.
They’ve quickly become a lunchbox favorite for my kids and my go-to breakfast with coffee (shoutout to my fellow iced latte ladies!). Plus, I love that they’re flexible enough to take on whatever mix-ins you’re craving (walnuts, pecans, chocolate chips… you name it). Bake a batch on Sunday and you’ve got healthy fall snacking sorted all week long.
- Whole wheat flour: Adds fiber and a subtle nutty flavor that makes these muffins more filling than those made with all-purpose flour. This recipe was developed specifically for whole wheat flour; if you swap in all-purpose, the texture and structure won’t be the same. Whole wheat absorbs more liquid, which is why these muffins turn out hearty without being heavy.
- Brown sugar: Just a half cup for the whole batch! Want a refined sugar–free option? Try coconut sugar for a 1:1 swap—it keeps the texture the same. Liquid sweeteners like maple syrup or honey will make the batter too wet and can lead to gummy muffins.
- Pumpkin pie spice: A full tablespoon brings big fall flavor without measuring out five separate jars of spice.
- Baking soda: Lifts the muffins so they bake up tall and fluffy.
- Pumpkin purée: I use canned pumpkin for convenience, but if you use homemade, be sure to drain it well. Fresh pumpkin is often more watery, which can make the batter too thin and the muffins gummy.
- Buttermilk: Adds moisture and a subtle tang for the most tender crumb, just like in my go-to Buttermilk Banana Bread. I used reduced-fat buttermilk here, but full-fat works, too. Don’t have buttermilk on hand? Check out my guide to buttermilk substitutes—I even share how to freeze buttermilk so you always have some ready for baking.
- Eggs: Bind everything together and give structure. Room temperature eggs will help the batter mix more evenly.
- Olive oil: My go-to healthy fat for moist, tender muffins. I stick with a mild olive oil so the flavor doesn’t come through, but melted coconut oil or avocado oil work great, too.
- Vanilla extract: Rounds out all the warm, cozy flavors.
- Mix-ins: Optional, but highly recommended! I love chopped walnuts, pecans or chocolate chips. You can even sprinkle pepitas or rolled oats on top before baking for extra crunch and texture.
See the recipe card for full information on ingredients and quantities.
- In a medium bowl, whisk together whole wheat flour, brown sugar, pumpkin pie spice, baking soda and salt.
- In another bowl, whisk together the pumpkin purée, buttermilk, eggs, olive oil and vanilla extract.
- Pour the wet ingredients into the dry and use a spatula or wooden spoon to gently fold until just combined. The batter should look thick and scoopable.
- If you’re adding any mix-ins, gently fold them in now. I like to save a small handful for sprinkling on top before baking to give the pumpkin muffins that baking-worthy finish.
- Scoop the batter into the lined muffin pan, filling each cup about ¾ full, then sprinkle a few extra mix-ins on top. Tip: A cookie scoop makes this quick and keeps the muffins uniform in size.
- Bake for 20 to 25 minutes in a 350°F oven, until the muffins are puffed, golden, and a toothpick inserted in the center comes out clean (a few moist crumbs are fine, just no wet batter).
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack. This quick rest keeps the bottoms from steaming and getting soggy. They’re incredible warm, but the flavor actually deepens after a few hours.
- Measure flour the right way. Use the spoon-and-level method: fluff the flour, spoon it into the cup, then level it off with a knife. Scooping straight from the bag can pack in way too much, which = dense, dry muffins. (Check out my video on how to measure flour accurately, and you’ll see the weight difference between spoon-and-level versus scooping straight from the bag.)
- Don’t overmix the batter. Once the wet and dry ingredients are combined, switch to a spatula or wooden spoon and stir gently. Overmixing develops gluten, which leads to tough muffins instead of light, fluffy ones. The batter should look mostly smooth with just a few streaks of flour—that’s your cue to stop mixing.
- You can use homemade pumpkin purée, but it usually contains more water, so you need to really drain it or the batter will be too thin.
Storage & Freezing
Store muffins in an airtight container for up to 2 days, or in the refrigerator for up to 5 days. If you refrigerate them, let them come to room temp or give them a quick warm-up in the microwave before serving for the best texture.
These healthy pumpkin muffins are freezer-friendly, too! I recommend wrapping each muffin individually in plastic wrap before stashing them in a zip-top bag or airtight container. Freeze for up to 3 months. Thaw overnight or warm in the microwave for 30 seconds.
Whether you snack on them plain, top them with a smear of cream cheese, or split one open and slather it with peanut butter (my personal favorite!), these healthy pumpkin muffins are the fall baking recipe you’ll make on repeat.
Ingredients
- 1 3/4 cups whole wheat flour
- 1/2 cup packed brown sugar
- 1 Tablespoon pumpkin pie spice
- 1 teaspoon baking soda
- 1/2 teaspoon kosher salt
- 1 1/2 cups pumpkin purée
- 1/2 cup reduced fat buttermilk
- 2 large eggs
- 1/4 cup extra-virgin olive oil
- 1 1/2 teaspoons vanilla extract
- 2/3 cup chopped walnuts, pecans or chocolate chips, plus more for topping
Instructions
- Preheat the oven to 350°F. Line a 12-cup muffin pan with baking cups.
- In a medium bowl, whisk together flour, brown sugar, pumpkin pie spice, baking soda and salt.
- In a separate medium bowl, whisk together the pumpkin purée, buttermilk, eggs, olive oil and vanilla extract.
- Add the wet ingredients to the dry ingredients and stir just until combined.
- Stir in the chopped nuts or chocolate chips (optional) then scoop the batter into the cups, filling each ¾ full.
- Bake the muffins until a toothpick inserted comes out clean, about 25 minutes. Remove them from the oven and allow them to cool in the pan for 5 minutes before transferring to a rack to cool completely.
Kelly’s Notes
- You can use homemade pumpkin purée, but it usually contains more water, so you need to really drain it or the batter will be too thin.
- Don’t overmix the batter. Once the wet and dry ingredients are combined, switch to a spatula or wooden spoon and stir gently. Overmixing develops gluten, which leads to tough muffins instead of light, fluffy ones. The batter should look mostly smooth with just a few streaks of flour—that’s your cue to stop mixing.
- To store: Store muffins in an airtight container for up to 2 days, or in the refrigerator for up to 5 days. If you refrigerate them, let them come to room temp or give them a quick warm-up in the microwave before serving for the best texture.
- To freeze: I recommend wrapping each muffin individually in plastic wrap before stashing them in a zip-top bag or airtight container. Freeze for up to 3 months. Thaw overnight or warm in the microwave for 30 seconds.
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