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Healthy Pumpkin Muffins

healthy pumpkin muffins recipe

We caught our first cool fall breeze this week. Do you know what that means? It’s pumpkin muffin time.

I snapped some new photos of my favorite pumpkin muffin recipe as I satisfied my pumpkin craving. These pumpkin muffins are perfect for chilly fall mornings and afternoon snacks.

They’re healthier than most, since they’re made with whole wheat flour and oats, sweetened with real maple syrup or honey, and call for coconut oil or olive oil instead of butter. Believe it or not, this healthy pumpkin muffin recipe yields light and fluffy muffins.

pumpkin muffin ingredients

These pumpkin muffins wouldn’t be complete without plenty of warming spices, including cinnamon, ginger and nutmeg. Most “pumpkin spice” flavor comes from the spice, not the pumpkin!

I love these muffins with a spread of almond butter, peanut butter or pecan butter on top. Nut butter adds some extra protein, which means that I’m not hungry before lunchtime. If you’re going pumpkin-crazy this time of year, enjoy your muffin with a homemade pumpkin chai latte.

These pumpkin treats have the magical power to convert “healthy muffin” skeptics into fans. Let’s make some!

how to make pumpkin muffins

The Best Pumpkin Muffins

Five reasons to love this pumpkin muffin recipe:

  1. These muffins are easy to make with basic ingredients. Only one bowl required!
  2. They’re made with 100% whole grains, yet they’re fluffy and delicious. No one will know the difference.
  3. They’re also naturally sweetened with maple syrup or honey, rather than loaded with refined sugar. The maple syrup (or honey) offers a touch of extra flavor, which I love.
  4. These muffins feature a few of your favorite warming spices so they taste like your favorite pumpkin latte.
  5. They freeze well for later, too. Just defrost individual muffins in the microwave for 30 to 60 seconds, or until gently warmed through. You don’t want to overdo it.

pumpkin muffin batter

Healthy Pumpkin Muffin Notes & Tips

Change it up. Add nuts, chocolate chips or chopped fruit cranberries or crystallized ginger. See recipe notes for details.

Simplify the recipe. Substitute 2 teaspoons store-bought pumpkin spice blend for the individual spices (cinnamon, ginger, nutmeg and allspice). Or, if your spice drawer is empty, simply use 1 1/2 teaspoons ground cinnamon and call it good.

Craving a sweet topping? Liz topped these muffins with my maple glaze from my pumpkin scones recipe, which sounds marvelous.

This muffin recipe is special diet-friendly. You can easily adjust this recipe to make it vegan, dairy free, egg free and/or gluten free. See the recipe notes for details.

whole grain, naturally sweetened pumpkin muffins

Baking Tips for Success

How to Measure Flour

How you measure your flour is important. Why? If you measure incorrectly, you could end up with up to 50 percent extra flour, which will make your muffins dense, dry and flavorless. Use the spoon and swoop method:

  1. Gently stir your flour to loosen any clumps.
  2. Spoon your flour into the measuring cup with a big spoon or a flour scoop. Do not scoop up the flour directly into the measuring cup.
  3. Level off the top of the cup with a knife. Repeat as necessary.

Use Baking Soda, Not Baking Powder

They are not the same thing. Both are leaveners that help your baked goods rise (baking powder contains some baking soda, but that’s a long story). For ideal results, always follow the recipe and measure carefully.

How to Stir Your Batter

This muffin batter is super simple to stir together by hand, and that’s how I recommend making these muffins. Why? Whipping your batter will make the flour’s gluten protein too strong, yielding tough muffins.

I know it can be tempting to use a stand mixer or hand mixer when it’s within reach. Please don’t! Follow the instructions below and you’ll end up with light, fluffy muffins.

Watch How to Make Healthy Pumpkin Muffins

pumpkin muffin recipe

Craving more wholesome muffins and pumpkin treats? You’re going to love these recipes:

  • Healthy Pumpkin Bread (like these muffins, but in bread form)
  • Pumpkin Pecan Scones with Maple Glaze
  • Pumpkin Pancakes
  • Healthy Banana Muffins
  • Healthy Apple Muffins

Please let me know how these pumpkin muffins turn out for you in the comments. I love hearing from you, and hope these pumpkin muffins become your new favorite.

P.s. That beautiful mug in the photos above and below? That’s handmade by my friend Margaret.

best healthy pumpkin muffins

Healthy Pumpkin Muffins

  • Author: Cookie and Kate
  • Prep Time: 10 mins
  • Cook Time: 23 mins
  • Total Time: 33 minutes
  • Yield: 12 muffins 1x
  • Category: Baked Good
  • Method: By hand
  • Cuisine: American

Easy, one bowl, healthier pumpkin muffins made with whole wheat grains and naturally sweetened! These pumpkin muffins are as light, fluffy and delicious as their coffee shop counterparts. Recipe yields 12 muffins.



  • ⅓ cup melted coconut oil or extra-virgin olive oil*
  • ½ cup maple syrup or honey
  • 2 eggs, at room temperature
  • 1 cup pumpkin purée
  • ¼ cup milk of choice (I used almond milk)
  • 2 teaspoons pumpkin spice blend (or 1 teaspoon ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, and ¼ teaspoon ground allspice or cloves)
  • 1 teaspoon baking soda
  • 1 teaspoon vanilla extract
  • ½ teaspoon salt
  • 1 ¾ cups whole wheat flour**
  • ⅓ cup old-fashioned oats, plus more for sprinkling on top
  • Optional: 2 teaspoons turbinado (raw) sugar for a sweet crunch


  1. Preheat oven to 325 degrees Fahrenheit (165 degrees Celsius). If necessary, grease all 12 cups of your muffin tin with butter or non-stick cooking spray (my pan is non-stick and didn’t require any grease).
  2. In a large bowl, beat the oil and maple syrup or honey together with a whisk. Add the eggs, and beat well. Add the pumpkin purée, milk, pumpkin spice blend, baking soda, vanilla extract and salt.
  3. Add the flour and oats to the bowl and mix with a large spoon, just until combined (a few lumps are ok). If you’d like to add any additional mix-ins***, like nuts, chocolate or dried fruit, fold them in now.
  4. Divide the batter evenly between the muffin cups. Sprinkle the tops of the muffins with about a tablespoon of oats, followed by a light sprinkle of raw sugar and/or pumpkin spice blend if you’d like. Bake muffins for 22 to 25 minutes, or until a toothpick inserted into a muffin comes out clean.
  5. Place the muffin tin on a cooling rack to cool. These muffins are delicate until they cool down. You might need to run a butter knife along the outer edge of the muffins to loosen them from the pan.
  6. These muffins taste even better after they have rested for a couple of hours! They’ll keep at room temperature for up to 2 days, or in the refrigerator for up to 4 days. They keep well in the freezer in a freezer-safe bag for up to 3 months (just defrost individual muffins as needed).


Recipe adapted from my honey-sweetened pumpkin bread.

*Oil options: I love coconut oil here. I used unrefined coconut oil and can hardly taste it in the final product. Olive oil might lend an herbal note to the muffins, if you’re into that (I tested with California Olive Ranch’s “Everyday” variety and couldn’t even taste it). Vegetable oil has a neutral flavor but the average vegetable/canola oil is highly processed, so I recommend using cold-pressed sunflower oil or grapeseed oil if possible.

**Flour alternatives: White whole wheat flour works great, if you can find it. Whole wheat pastry flour yields extra light and fluffy muffins that are delicate until cooled. All-purpose flour and gluten-free all-purpose flour blends work as well.

**Change it up: You could really go crazy with add-ins here. After stirring in the flour and oats, gently fold in up to ¾ cup chocolate chips, chopped nuts like pecans or walnuts, and/or some chopped dried cranberries or crystallized ginger.

Serving suggestions: These muffins are great on their own, with a pat of butter, or spread with almond butter. They would also be fantastic with homemade pecan butter or coconut butter.
Make it egg free: Readers report that these muffins turn out well with flax eggs!
Make it vegan: Use maple syrup, flax eggs and non-dairy milk.
Make it dairy free: Simply use your non-dairy milk of choice.
Make it gluten free: Bob’s Red Mill gluten-free all-purpose blend works well instead of the whole wheat flour.

Make it oat free: Simply omit the oats. No other changes necessary.

Make it lower in fat: I would argue that this bread contains a healthy amount of fat, but you can replace the oil with applesauce if you’re following a low-fat diet. Choosing olive oil instead of coconut oil will reduce the saturated fat content; total fat content will remain the same.

Update September 24, 2019: I removed white whole wheat flour as an option simply because I can’t find it in stores any more. I also upped the amount of spice from 1 ½ teaspoons to 2 teaspoons.

▸ Nutrition Information

The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice.


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