These healthy pumpkin muffins are made with Greek yogurt and whole wheat flour for a soft and tender muffin recipe. You'll never know that these pumpkin yogurt muffins are sweetened only with maple syrup.
Pumpkin muffins are a classic two-bowl, hand-mix, pour the wet into the dry kind of easy recipe. And with a bake time roughly 45 minutes less than pumpkin bread, they're sometimes just what you feel like making.
A fall staple, I tweaked my aforementioned pumpkin bread recipe into a batch of 12 healthy pumpkin muffins for a reliably moist and tender result. These hit the spot for breakfast or a snack.
Reasons to Love This Recipe
- Making pumpkin muffins with Greek yogurt means they're so moist, and stay that way until all the leftovers are eaten. This also means you can cut down on added oil.
- They're made with all whole wheat flour, but you'd never know. This bumps up the whole grains.
- The only sugar content comes from maple syrup and plain Greek yogurt, meaning these muffins are all naturally-sweetened.
- White Whole Wheat Flour: This is produced using white wheat instead of red wheat, which is what traditional whole wheat flour is made from. White whole wheat is lighter in color and in flavor, and it still contains wheat bran and wheat germ, unlike all-purpose flour. (Source: The Kitchn)
- Pumpkin Puree: Make sure to use puree and not canned pumpkin pie filling, which is pre-spiced and sweetened.
- Maple Syrup: Use pure maple syrup and not a breakfast/pancake type syrup here.
- Greek Yogurt: Plain whole milk (5%-ish) Greek yogurt is recommended, though a lower-fat (around 2% or so) is okay to use as we're also adding oil to this recipe.
- Oil: Any neutrally-flavored cooking oil you like to use is fine: vegetable, canola, melted coconut oil or unsalted butter, etc.
- Pumpkin Pie Spice: The recipe card calls for a pre-made/homemade blend, but also includes quantities of individual spices if you'd rather make it yourself.
- Dry Ingredients - In one mixing bowl, whisk together the flour, pumpkin pie spice, baking powder, salt, and baking soda.
- Wet Ingredients - In a separate mixing bowl, whisk together the pumpkin puree, maple syrup, Greek yogurt, oil, eggs, and vanilla extract until smooth.
- Combine - Pour the wet ingredients into the dry ingredients and stir by hand until evenly combined. Stir in the chia seeds.
- Scoop - Evenly portion out the batter into a greased muffin tin, smoothing out the surface. A cookie scoop makes scooping muffin batter less messy.
- Bake - Bake these whole wheat pumpkin muffins on the middle rack of a 350°F oven for 18-20 minutes, or until a tester inserted into the center of the tallest muffin comes out clean. Let them cool in the pan for 5 minutes then transfer to a wire rack to cool completely.
Recipe Tips and Tricks
- Measuring Flour - Do this by stirring up the flour in itself container and spooning it into your dry measuring cup. Level off the top with a straight edge, letting the excess fall back into the bag. This prevents the flour from being packed in, which can result in drier-than-ideal baked goods.
- Muffin Liners - I've tested these whole wheat pumpkin muffins with paper muffin liners and found that their lower fat content led to them sticking to the liners a bit too much. I recommend just greasing a pan.
- Dark vs. Light Metal Pans - Dark metal pans heat up more quickly than light metal pans, so if using one you'll want to check on these muffins on the earlier end of the range.
- Mini Pumpkin Yogurt Muffins - This recipe will produce roughly 36-40 mini muffins. Bake at the same temperature, but reduce the bake time to 10-11 minutes total.
After they've cooled completely, store these healthy pumpkin muffins in an air-tight container (or sealable bag with excess air pressed out) at room temperature for up to 3 days. They also freeze in the same manner for 3 months. As time goes by they'll become moister, so I like to lightly wrap a paper towel along the top and bottom surfaces of the muffins to absorb some of the moisture that accumulates.
You can replace a portion of the maple syrup with honey, use all-purpose or regular whole wheat flour, use melted butter in place of oil, use a flax egg in place of one of the regular eggs, use a different blend of spices, omit the chia seeds, etc. This easy recipe lends itself well to customization.
Check out my full list of canned pumpkin recipes to make this fall, organized by amount to help you deliciously use up a can of pumpkin.
If you’ve enjoyed this recipe, I’d love for you to leave a star rating in the recipe card and/or a comment review below!
Healthy Pumpkin Muffins
- 2 cups white whole wheat flour spooned and leveled
- 5 teaspoons pumpkin pie spice
- 2 teaspoons baking powder
- ½ teaspoon salt
- ¼ teaspoon baking soda
- 1 cup pumpkin puree
- ⅔ cup maple syrup
- ½ cup plain Greek yogurt whole milk recommended, low-fat fine
- ¼ cup neutral-tasting oil such as canola or melted coconut oil
- 2 large eggs
- 1 ½ teaspoons vanilla extract
- 3 Tablespoons chia seeds (whole)
- Preheat oven to 350°F (177°C) and spray a regular-sized 12-cup muffin tin with cooking spray.
- In a large mixing bowl, add flour, pumpkin pie spice, baking powder, salt, and baking soda. Whisk to combine evenly.
- In a separate mixing bowl, add pumpkin puree, maple syrup, Greek yogurt, oil, eggs, and vanilla extract and mix until smooth and combined. You can use a hand mixer if you like, but I usually just use a whisk and mix by hand.
- Pour the wet ingredients into the bowl with the dry ingredients and stir until just combined. Some lumps in the batter are okay. Gently stir in the chia seeds, taking care not to over-mix.
- Portion out the batter evenly into the greased muffin tin. I like to use a cookie scoop to help make this process more efficient with less drips.
- Bake for 18-20 minutes, or until a tester inserted into the center of a muffin comes out clean and the tops spring back when lightly pressed.
- Let muffins cool in the muffin tin for 5 minutes, then carefully loosen the edges with a small spatula and transfer to a wire rack for them to cool completely.
- Spoon and Level Flour - To measure the flour correctly, stir up the flour in its container to "fluff" it up. Then spoon it into your measuring cup, taking care not to compress it down. Continue until the measuring cup is overflowing, then use a straight edge to level off the measuring cup.
- Mini Muffins - This recipe should produce between 36-40 mini muffins. Bake at the same temperature but reduce the bake time to 10-11 minutes.
- Storing Instructions - Once cooled store in an air-tight container or bag at room temperature for 3 days, or freeze for 3 months. Line the top and bottom of the container with a paper towel to absorb excess moisture that develops, replacing it as needed.
- Pumpkin Pie Spice - If you don't have this pre-blended, use the following quantities:
- 2 ½ teaspoons ground cinnamon
- ¾ teaspoon ground ginger
- ¾ teaspoon ground nutmeg
- ½ teaspoon ground allspice
- ½ teaspoon ground cloves
Diane Meyer says
I am always looking for recipes to use my homegrown and processed pumpkin; this recipe did not disappoint! I did use nonfat plain greek yogurt as that is what I eat. The muffins were as moist as I would expect them to be.
I'm so happy you liked them, Diane! Thanks for letting me know how they went. 🙂
Great recipe! Has a very healthy taste and I added chopped pecans instead of chia seeds. (I think oats or poppyseeds will add good textures too). At first I was taken a back by how not so sweet (I’m used to costco muffins) the muffins were but quickly got used to and started enjoying that subtle sweetness! (Could add more maple syrup if you like sweet muffins). Thank you for sharing this
So glad you liked them! Pecans sound like a wonderful addition, and I definitely know what you mean about the Costco muffin comparison.
When it says 1 can of pumpkin purée, what size can?
Hi Sariah, one cup of pumpkin puree (not can) is used here. 🙂
The instructions don’t indicate what to do with the chia seeds. Are they intended to go in whole or do you grind them?
Thank you for catching that! I will add it to the recipe card. They're folded into the batter (whole) right before it gets poured into the muffin tin.