Whole Wheat Pumpkin Muffins

These whole wheat pumpkin muffins are perfectly spiced, not too sweet, relatively healthy, and easy to make thanks to canned pumpkin. You just may find yourself making these all year long as well as on Thanksgiving morning.

A muffin tin filled with pumpkin muffins in paper liners.

These healthy pumpkin muffins are the perfect answer for anyone who may feel a touch sheepish about indulging in a pumpkin pie for breakfast. Thanks to canned pumpkin and pumpkin pie spice, you’ll find all the familiar flavors of Thanksgiving in these muffins. Whole wheat flour and homemade pumpkin seed flour ensure an enticingly tender crumb and velvety texture. And a smidgen of honey and brown sugar ensure they’re sufficiently sweet. So lovely you just may find yourself craving them all year long.–Angie Zoobkoff

Pumpkin Muffin FAQs

How should I serve these whole wheat pumpkin muffins?

Serve them warm, with a regular or nut butter. If you love warm autumn spices, try them with this homemade cinnamon butter.

Can I freeze these muffins?

Definitely. Stash the cooled muffins in a resealable bag and store them for up to 3 months. Defrost in the microwave for a quick on-the-go breakfast.

Whole Wheat Pumpkin Muffins

A muffin tin filled with pumpkin muffins in paper liners.
These helathy whole wheat muffins are perfectly spiced, not too sweet, and easy to make. You just may find yourself making these all year long as well as on Thanksgiving morning.

Prep 30 minutes
Cook 30 minutes
Total 1 hour
12 muffins
260 kcal
4.75 / 4 votes
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  • Paper baking cups (optional)


  • 3/4 cup (3 oz) raw shelled pumpkin seeds (pepitas)
  • 1 1/3 cups whole wheat pastry flour
  • 1/4 cup packed brown sugar
  • 1 1/2 teaspoons baking soda
  • 1 teaspoon baking powder
  • 1 tablespoon store-bought or homemade pumpkin pie spice
  • 1/2 teaspoon kosher salt
  • 1 large egg
  • 3/4 cup homemade or canned plain pumpkin purée (not pumpkin pie filling)
  • 1/4 cup whole or 2% milk
  • 1/2 cup honey
  • 1/3 cup canola oil or grapeseed oil plus more for the muffin cups


  • Preheat the oven to 350ºF (177ºC). Slick a 12-muffin pan with oil or line it with paper baking cups.
  • Toss the pumpkin seeds into a food processor, high-powered blender, or coffee grinder and pulse until they’re the texture of flour, being careful not to overdo it or you’ll end up with pumpkin seed butter.
  • Scrape the pumpkin seed flour into a large bowl and add the whole wheat pastry flour, brown sugar, baking soda, baking powder, pumpkin pie spice, and salt. Whisk well to combine.
  • In a smaller bowl, whisk together the egg, pumpkin purée, milk, honey, and oil until smooth and combined. Pour this pumpkin mixture over the flour mixture and stir with a rubber spatula just until smooth with no streaks of flour remain. Scrape the batter into the prepared muffin cups.
  • Bake the pumpkin muffins for 15 to 20 minutes, until just firm to the touch and a toothpick inserted in the center comes out clean.
  • Let the muffins cool in the pan on a wire rack for a few minutes. If not using paper baking cups, run a knife around the edge of each muffin. Gently turn each muffin out of the pan and onto the wire rack and cool completely. (The muffins will remain moist and tender for up to 3 days when stored in a closed container at room temperature.)
Print RecipeBuy the Rise and Shine cookbook

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Show Nutrition

Serving: 1muffinCalories: 260kcal (13%)Carbohydrates: 29g (10%)Protein: 7g (14%)Fat: 14g (22%)Saturated Fat: 2g (13%)Polyunsaturated Fat: 5gMonounsaturated Fat: 7gTrans Fat: 1gCholesterol: 16mg (5%)Sodium: 246mg (11%)Potassium: 262mg (7%)Fiber: 3g (13%)Sugar: 17g (19%)Vitamin A: 2419IU (48%)Vitamin C: 1mg (1%)Calcium: 46mg (5%)Iron: 2mg (11%)

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Recipe Testers’ Reviews

These healthy pumpkin muffins were moist, spicy, not too sweet, and had an almost velvety texture from the ground pumpkin seeds that was similar to baked goods made with almond flour. They were not crumbly at all. The muffins smelled very strongly of honey when they were hot, but the honey flavor was very subtle, letting the pumpkin and spices shine. They were perfect with no additional adornments and at room temperature—just right to grab for a quick weekday breakfast.

And they were great keepers—they were still quite moist 4 days after I made them. I froze some of them and when they thawed they were as moist as the day I made them. I will definitely be making these again. I used a coffee grinder instead of a blender to grind the pumpkin seeds. It worked beautifully, though I should have ground the seeds in two smaller batches instead of one big one.

These whole wheat pumpkin muffins were everything that I wanted them to be. They were so good that I ate them for breakfast, dessert, and as a snack. The whole wheat pastry flour combined with the ground pepitas made a nice texture. I pulsed the pepitas for about 1 minute to achieve the right texture though I might leave a few larger pieces of the pepitas next time for a little extra contrast in texture.

Because I used paper liners, they were very easy to get out of the pan and I did not experience any issues with them falling apart.

There are several things I really liked about these flavorful whole wheat pumpkin muffins. First, the mixture of whole wheat flour and homemade pepita flour for the base; second, the lovely fall flavor of pumpkin purée and pumpkin spice mix; next, the texture of the muffins; and last, the fact that you don’t need to add any butter to the mixture to achieve the deliciousness! I think the combo of oil and pumpkin purée really gives these muffins a lovely moist crumb, not to mention the slight nutty texture from the homemade pepita flour.

The use of honey and brown sugar as the sweeteners really gave it a nice underlying sweetness—I say this because the muffins aren’t overly sweet but sweet enough to let the pumpkin flavor shine through.

Overall, a lovely muffin that has me excited for warm, rich, fall flavors!

I’m one of those people who loves pumpkin everything. These whole wheat pumpkin muffins are extra fun because they also use pumpkin seeds. Grinding up the pepitas is easy and a fun substitution for something like almond meal. It helps to keep the muffins moist and offers a little more nutrition.

They were also not too sweet, which means you have room to enjoy one with a nice rich cup of chai. I kept the extra muffins in the fridge for a couple of days and they almost got a sticky toffee pudding texture.

Pumpkin muffins are one of my favorite quick breads, especially if they’re a bit dense and not too cake-like sweet. These deliver exactly what I love. The sweetness is kept in check with brown sugar and honey, the texture is tender but not light and fluffy, and they have a nice, dense texture that proper muffins should have. The idea of using ground-up pumpkin seeds for flavor and texture is a great trick and gives these a definite edge.

The fact that they are more nutritious than your standard version is a nice plus. I used my Vitamix to grind the pumpkin seeds. I blended them for 30 seconds total in 10 second increments, shaking the blender in between. This worked great.

Just a quick update: Sure these whole wheat pumpkin muffins are delicious the day they are baked but they also keep really well. I ate the last one (stored on our cake stand with a lid along with other baked goods) yesterday and I had initially baked this batch several days prior!

There’s nothing like a hearty quick bread stuffed with sweet spices in the fall. With the whole wheat flour and fresh pumpkin purée, these didn’t feel quite like eating glorified cupcakes like some muffins do. The texture was super tender yet the muffins stayed together and didn’t crumble apart while I was eating them. They would make an excellent canvas for the addition of raisins, walnuts, diced apples, or any other favorite fall mix-in.

The pumpkin seeds took about 60 seconds to turn flour-like in the food processor. I roasted a small sugar pumpkin by slicing it lengthwise, scooping out the seeds, and lightly brushing with canola oil before baking for about 1 hour at 400°F. The flesh becomes very tender. I allowed it to cool for about 20 minutes before scooping into a food processor and puréeing for 2 minutes until very smooth. I used about half the purée for the muffins and froze the other half.

The rest of the ingredients came together easily as a fairly simple muffin batter. The muffins stayed fresh in a Tupperware for about 3 days. I’m sure they would freeze well also.

This whole wheat pumpkin muffin recipe was easy to make and tasted good. I like the fact that there are finely ground pumpkin seeds in the muffins because it adds fiber and nutrition. I might play with adding something fun, like golden raisins, or reducing the seeds and adding nuts or even chocolate chips and a streusel topping.

Originally published November 19, 2016


#leitesculinaria on Instagram If you make this recipe, snap a photo and hashtag it #LeitesCulinaria. We'd love to see your creations on Instagram, Facebook, and Twitter.


    1. Hi Vanessa! You could try using half all-purpose and half whole wheat flour in place of the whole wheat pastry flour. Do let us know how they turn out!

  1. 5 stars
    These pumpkin muffins are delicious and easy to make. Ground pepitias–BRILLIANT idea. I substituted golden monk fruit sweetener for the brown sugar to cut back on the sugar content a bit. Honey adds both sweetness and moisture, but I wonder if I could substitute monk fruit sweetener for some of it. Might try that next time. I’ll be making these again, many times.

    1. Love to hear this, Russ. Thanks so much for sharing this! None of us has baked with monk fruit sweetener, but we worked with tapioca syrup, and I suspect you could swap it for some of it, just beware, the moisture content will be slightly different, so maybe experiment a little but start on the side of caution. Let us know how it goes!

  2. 5 stars
    After reading all the very positive reviews, I just had to try the recipe but with a big twist. I love pumpkin but I wanted to try with gluten free flour. The result was very successful. I just wanted to share this for those who might be on gluten free diets. The only substitute I made was 1 1/3 cups Bob’s Red Mill GF All Purpose Flour, and 3/4 tsp xanthan gum. That’s it. Perfect muffins, very light and moist. A definite winner.
    If I made a second time, I’ll increase the sugar a bit, as perhaps the flour substitution reduced the sweetness, but still can enjoy the muffin with some honey or jam to make up for the sweetness. This is my first time substituting GF flour for regular wheat flour. The result is not bad.
    Thank you so much for sharing.

    1. Elizabeth, we can’t thank you enough for this incredibly helpful information. We often get queries regarding substituting gluten-free flour in recipes, and it’s so nice to be able to confidently answer. We’re so pleased that you enjoyed them!

    1. You should be able to swap in all purpose flour here, Carol. We recommend using weight measurements if possible, and if your batter seems a touch dry, add a little bit more milk. Do let us know how they turn out!

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