Dessert

Whole Wheat Pumpkin Muffins Recipe

ByMaya Quinn February 4, 2026February 4, 2026

Introduction

These Whole Wheat Pumpkin Muffins are a wholesome twist on a classic fall treat. Packed with warm spices and a crunchy pecan topping, they offer a perfect balance of moistness and texture. Ideal for breakfast or a cozy snack, they bring autumn flavors right to your kitchen.

The image shows three crumb-topped muffins placed closely together on a stack of three white plates with a smooth finish. Each muffin has two layers: the base layer is a light brown cake wrapped in a white paper liner with visible brown specks, and the top layer is a thick, crumbly, golden brown streusel topping with small nut pieces scattered throughout. The background includes a white marbled surface and a soft-focus view of more muffins on a cooling rack. Some crumbs and small nut fragments are scattered around the plates, and a blue and white striped cloth is partially visible in the lower-left corner. Photo taken with an iphone --ar 4:5 --v 7

Ingredients

1 egg
½ cup unsalted butter (melted)
1 ¼ cup sugar
1 cup pumpkin puree
2 tablespoons plain yoghurt
1 cup whole wheat flour
½ cup all-purpose flour
¼ cup wheat germ
½ cup bran
2 teaspoons pumpkin spice
1 teaspoon baking powder
½ teaspoon baking soda
½ teaspoon salt
3 tablespoons butter (melted)
½ cup brown sugar
½ cup flour
1 teaspoon cinnamon
½ cup pecans (chopped)

Instructions

Step 1: Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners and set aside.
Step 2: In a large bowl, whisk together the egg, ½ cup melted butter, and sugar until well combined. Stir in the pumpkin puree and yoghurt, then set aside.
Step 3: In a separate large bowl, whisk together whole wheat flour, all-purpose flour, wheat germ, bran, pumpkin spice, baking powder, baking soda, and salt.
Step 4: Gradually add the dry flour mixture to the wet pumpkin mixture, stirring gently until just incorporated.
Step 5: Scoop the batter into the prepared muffin cups, filling each about ¾ full.
Step 6: In a medium bowl, combine the melted butter, brown sugar, flour, cinnamon, and chopped pecans. Mix until it forms coarse crumbs.
Step 7: Sprinkle the crumb topping evenly over each muffin.
Step 8: Bake for 25 minutes or until a toothpick inserted into the center comes out clean.
Step 9: Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely.

Tips & Variations

For extra moisture, swap plain yoghurt with Greek yoghurt or sour cream.
Use chopped walnuts instead of pecans for a different nutty flavor.
Add a handful of chocolate chips or dried cranberries to the batter for a sweet surprise.
Make sure not to overmix the batter to keep the muffins tender and light.

Storage

Store these muffins in an airtight container at room temperature for up to 3 days. For longer storage, freeze the muffins in a sealed bag for up to 2 months. To reheat, thaw at room temperature and warm in a microwave for 15–20 seconds.

How to Serve

Thirteen round muffins with a crumbly, textured topping cover the entire muffin tops in uneven clumps of light and dark brown with bits of pecans visible, arranged on a black wire cooling rack. The muffins are golden brown with a soft, slightly rough surface showing beneath the crumb topping. The rack sits on a white marbled surface, with a blue and white striped cloth partially visible on the left side. Small crumbs are scattered around the muffins and rack, adding to the rustic look. Photo taken with an iphone --ar 4:5 --v 7

Serve this delicious recipe with your favorite sides.

FAQs

Can I use canned pumpkin puree for this recipe?

Yes, canned pumpkin puree works perfectly and is the standard choice for pumpkin baking recipes.

Are these muffins gluten-free?

No, these muffins contain whole wheat flour and all-purpose flour, which both contain gluten. For a gluten-free version, you would need to substitute these with gluten-free flour blends.