Recipes > Breakfast > Whole Wheat Pumpkin Muffins

Whole Wheat Pumpkin Muffins

These whole wheat pumpkin muffins are made with whole wheat flour & are lower in sugar than traditional muffin mixes or store bought muffins.
whole wheat pumpkin muffins in a muffin tin

This is a variation of our whole wheat muffins base recipe. 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!

Three Must Know Cooking Skills

For recipe success, learn how to:

Measure Flour
Mix Using The Muffin
Measure Brown Sugar

Culinary Tips for Fluffy Pumpkin Muffins

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.

When measuring brown sugar, pack it in the cup. If you add the chocolate chips or prefer a less sweet muffin, reduce the sugar to 1/3 cup. The recipe will still come out great!

Don’t overmix the batter! Overmixing creates dense and tough muffins. 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.

Use a portion scoop to distribute the batter into the muffin tins. This handy tool can help make perfect muffins, cupcakes, pancakes, and more. It also makes the work easier; just squeeze the handle, and the batter slides right out!

We used a dark non-stick muffin pan to bake these muffins. If you use a light colored pan, the cooking time will increase. To check for doneness, insert a toothpick into a muffin in the middle of the pan. If it comes out clean, it’s done! 

Ingredient Substitutions

  • White Whole Wheat Flour: substitute whole wheat pastry flour or spelt flour for a similarly light taste, color, and texture. You can also substitute 1 cup whole wheat flour and ½ cup all-purpose flour. We don’t recommend subbing all regular whole wheat flour, as the muffins will come out dense and grainy.
  • 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. You can also just substitute cinnamon or apple pie spice.
  • Pumpkin: substitute mashed sweet potatoes or pureed butternut squash. (Although then it wouldn’t be pumpkin muffins…)
  • Brown Sugar: substitute cane sugar, but note that the flavor will be slightly different. 
  • Eggs: to make vegan muffins, substitute the eggs with flax eggs. 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 a vegan version might not be quite as fluffy.
  • Canola Oil: substitute avocado oil. Do not substitute olive oil, as this has a strong flavor. Do not substitute vegetable oil, as this is not a heart-healthy oil.

We love buying our spices from The Spice House. Click on the picture below to view & try out hundreds of flavorful spices and herbs!

row of spices

Recipe Variations

Turn these into high fiber muffins by adding 2 Tablespoons ground flaxseed (flaxseed mill) to the dry ingredients or topping the muffins with pumpkin seeds before cooking.

Make oatmeal pumpkin muffins by substituting ½ of the whole wheat flour with oat flour. This will slightly alter the texture.

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 1/3 cup. If you’re a chocoholic, you’ll love this variation! Note that adding chocolate chips will increase the yield, so bake extra batter in silicone liners.

For fun-sized pumpkin muffins, use a mini muffin pan! Prepare with mini muffin liners or non-stick spray and bake for 10-12 minutes, or until a toothpick inserted comes out clean.

This batter works for quick bread too! To make whole wheat pumpkin bread, prepare a 9×5 loaf pan with parchment paper or non-stick spray. Cook for 50-55 minutes, or until a toothpick inserted into the middle comes out clean. 

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

Equipment Recommendations

You just need a few pieces of equipment for this recipe:

Are pumpkin 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 ~2 teaspoons (8 grams) of added sugar. 

Serving Suggestions

We doubt you’ll be able to resist biting into a warm, fluffy muffin when it’s fresh out of the oven! 

Top pumpkin 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

Because these are moist muffins, they will spoil more quickly at room temperature. Cool completely, then 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 Pancakes Base Recipe

Overnight Oats Base Recipe

Homemade Granola Base Recipe

Baked Oatmeal Cups Base Recipe

whole wheat pumpkin muffins in a muffin tin

Whole Wheat Pumpkin Muffins

This is a variation of our whole wheat muffins base recipe. 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!
5 from 1 vote
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American
Servings 12 muffins


  • 1 ½ cups white whole wheat flour*
  • ½ Tablespoon pumpkin pie spice
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • ½ teaspoon kosher salt
  • ½ cup dark chocolate chips (optional)
  • 15- ounce can pure pumpkin
  • ½ cup packed brown sugar
  • ¼ cup canola oil
  • 2 large eggs
  • 1 teaspoon vanilla extract


  • Preheat oven to 350° F. Prepare a 12-cup muffin pan with nonstick spray or muffin liners.
  • In a large bowl, gently whisk whole wheat flour, pumpkin spice, baking soda, baking powder, salt, and optional chocolate chips.
  • In a separate large bowl, whisk pumpkin, sugar, oil, eggs, and vanilla until combined.
  • Add pumpkin mixture to flour mixture. Using a spatula, fold ingredients until just moistened. Do not overmix.
  • Portion ~¼ cup batter into each cup. Bake 18-20 minutes or until slightly golden and a toothpick inserted into the middle comes out clean. Enjoy!


*Substitute 1 cup whole wheat flour and 1/2 cup all purpose flour.
Adding chocolate chips will yield ~14 muffins instead of 12.
Keyword Whole Wheat Pumpkin Muffins

This Post Has 6 Comments

  1. Sherry varga

    You mention all purpose flour in directions, but it is not listed in ingredients!

    1. Great catch! We have gone back & adjusted this recipe to match our base recipe, but neglected to take that direction out. It’s fixed now! You can either use 1 1/2 cups white whole wheat flour, or 1 cup whole wheat + 1/2 cup all purpose for best texture, taste, and nutrition.

  2. Charlotte

    Is there buttermilk in the recipe? Didn’t see it on the list.

    1. There is now! Thank you for that catch; we are currently updating old recipe posts to match our base recipe, and that one slipped through the cracks! I hope you enjoy the recipe.

  3. Debra

    Used the 1/2 cup white flour and one cup whole wheat. Loved the muffins.

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