Healthy Pumpkin Muffins with Yogurt

Name: Healthy Pumpkin Muffins
Prep time: 16 min
Cook time: 18 min
Total time: 34 min
Ingredients: 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))

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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 on a serving board with a bite taken out of one.

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.

Baked pumpkin muffins in a metal muffin tin.

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.

Recipe Ingredients

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.

Step-by-Step Instructions

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.

Whisks in two bowls of mixed ingredients: dry on the left and wet on the right.

Combine - Pour the wet ingredients into the dry ingredients and stir by hand until evenly combined. Stir in the chia seeds.

Pumpkin muffin batter and a spatula in a mixing bowl.

Scoop - Evenly portion out the batter into a greased muffin tin, smoothing out the surface. A cookie scoop makes scooping muffin batter less messy.

Batter portioned out into a metal muffin pan.

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.

Recipe FAQs

How do you best store whole wheat pumpkin muffins?

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.

How can I switch up this recipe?

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!