Whole Wheat Pumpkin Muffins

Pumpkin may be the taste of fall, but these whole wheat pumpkin muffins can be made all year round! These easy pumpkin muffins are made with whole wheat flour and are lower in sugar than traditional muffin mixes or store bought muffins. They’re moist, delicious and hard to mess up! Plus, they use the whole can of pumpkin, so you aren’t left with an awkward leftover amount that you don’t know what to do with! Give these healthy muffins a try, then be sure to give us a review!

Are muffins healthy?

Well, that depends. Many muffin mixes contain way too much added sugar. Some even contain up to or even more than your daily allowance of sugar – yikes!

The key nutrients that make these whole wheat pumpkin muffins healthier are whole wheat flour, pumpkin puree, and less sugar than leading brands.

Whole Wheat Flour

Whole wheat flour is a good source of fiber, B vitamins, Vitamin E, trace minerals, and phytochemicals. Replacing refined grains (i.e. white flour) with whole grains (i.e. whole wheat flour) may reduce the risk of developing chronic conditions such as heart disease, diabetes, and certain types of cancer (1). 

Pumpkin Puree

Pumpkin is a great source of beta carotene, fiber, and potassium. These nutrients promote immune function, gut health, good cholesterol, and normal blood pressure. Be sure to purchase pure pumpkin puree and not canned pumpkin pie filling, as this contains added sugar.

Less added sugar than leading brands

High sugar consumption is not good for health, and in general, most Americans eat way too much. Men should aim to consume less than 9 teaspoons (~36 grams) of sugar per day, and women should aim to consume less than 6 teaspoons (~24 grams) of sugar per day (2). Each muffin in this recipe has 3 teaspoons (12 grams) of added sugar. 

Equipment Recommendations

This spatula is one of Chef V’s favorite kitchen utensils. It’s perfect for scooping pumpkin out of the can AND for mixing the batter together!

To make evenly-sized muffins, use a portion scoop! This handy tool can help you make perfect muffins, cupcakes, pancakes, and more. It also makes the work easier; just squeeze the handle, and the batter slides right out!

For fun-sized pumpkin muffins, use a mini muffin tin! Keep in mind that cooking time will decrease.

Culinary Tips

Measure the flour properly to prevent dense muffins. Fluff, spoon, and level; don’t scoop and pack! 

Whisking the dry ingredients together mimics sifting, so don’t substitute another utensil.

Don’t overmix the batter! Watch our muffin method culinary technique video to learn how to mix the muffin batter just enough so that you end up with light and fluffy muffins.

We used a dark non-stick muffin pan to bake these muffins. If you use a light colored pan, the cooking time will increase.

When measuring brown sugar, pack it in the cup. If you don’t have much of a sweet tooth or prefer a less sweet muffin, reduce the sugar to ½ cup. The recipe will still come out great!

Ingredient Substitutions

  • Whole wheat flour: use white whole flour or whole wheat pastry flour for a lighter taste, color, and texture. Make oatmeal pumpkin muffins by substituting ½ of the whole wheat flour with oat flour. This will slightly alter the texture.
  • Pumpkin pie spice: don’t have pumpkin pie spice on hand? No problem! You can make your own by mixing together cinnamon, ginger, ground cloves, and nutmeg.
  • Pumpkin: substitute mashed sweet potatoes. (Although then it wouldn’t be pumpkin muffins…)
  • Eggs: substitute the eggs with flax eggs to make vegan pumpkin muffins. To make one flax egg, mix 1 Tablespoon of ground flaxseeds with 3 Tablespoons of water and let it rest for 10 minutes. Eggs help leaven the muffins, so vegan muffins might not be quite as fluffy. 

Recipe Variations

Turn these into high fiber muffins by adding 2 Tablespoons ground flaxseed (flaxseed mill) to the dry ingredients, using only whole wheat flour (the muffins won’t be as fluffy), or topping the batter with pumpkin seeds. If using only whole wheat flour, we recommend white whole wheat flour or whole wheat pastry flour.

Want to make a larger quantity or not scoop out individual muffins? Check out our whole wheat pumpkin bar recipe! It’s essentially the same recipe, just cut into squares!

Make whole wheat pumpkin chocolate chip muffins by folding ½ cup semisweet or dark chocolate chips into the batter. This increases the sweetness of the recipe, so we recommend reducing the sugar to ½ cup (instead of ¾ cup). If you’re a chocoholic, you’ll love this variation!

Serving Suggestions

Top these muffins with some almond butter or serve with fruit and yogurt for a balanced breakfast, eat them on their own for a light snack, or enjoy as a tasty treat at lunch.

What to do with Leftover Pumpkin Muffins

Store the muffins in a bag or container at room temperature for a few days or in the refrigerator for up to one week.

Got a busy few weeks ahead? These muffins are great for the freezer! Cool completely, wrap individually or in pairs, and then store in a freezer-safe bag for up to 3 months. When ready to eat, thaw overnight in the refrigerator, or reheat in the microwave in the morning!

Want more healthy whole grain recipes?

Check out these healthy twists on classic favorites! 

Whole Grain Pancake Base Recipe

Overnight Oats Base Recipe

Homemade Granola Base Recipe

Baked Oatmeal Cups Base Recipe

Whole Wheat Pumpkin Muffins
Prep Time
10 mins
Cook Time
20 mins
Total Time
30 mins

These easy whole wheat pumpkin muffins use one full can of pumpkin, so they are extra moist AND you won't be stuck with an awkward leftover amount of pumpkin!

Course: Breakfast
Cuisine: American
Yield: 12 muffins
  • 1 cup whole wheat flour
  • ½ cup all purpose flour
  • ½ Tablespoon pumpkin pie spice
  • 1 teaspoon baking soda
  • ¾ teaspoon salt
  • ½ teaspoon baking powder
  • 1- 15 ounce can pure pumpkin
  • ¾ cup brown sugar
  • 2 large eggs
  • ¼ cup canola oil
  1. Preheat oven to 350° F. Prepare a 12-cup muffin pan with nonstick spray or muffin liners.

  2. In a large bowl, gently whisk whole wheat flour, all purpose flour, pumpkin spice, baking soda, salt, and baking powder. 

  3. In a separate large bowl, whisk pumpkin, sugar, eggs and oil until combined.

  4. Add pumpkin mixture to flour mixture. Using a spatula, fold ingredients until just moistened. Do not overmix.

  5. Portion about ¼ cup batter into each cup. Bake 15-20 minutes or until slightly golden and a toothpick inserted into the middle comes out clean. Enjoy!

Recipe Notes

Optional ingredients:

½ cup chocolate chips

Consider reducing the sugar to ½ cup when adding chocolate chips.

Adding chocolate chips will yield ~14 muffins instead of 12.

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