Whole Wheat Pumpkin Muffins

5 from 1 vote

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Pumpkin muffins, but make it healthy! You are going to love these Whole Wheat Pumpkin Muffins that are light, moist and make the perfect breakfast or snack. 

Pumpkin anything fills my soul. The smell, the taste, it’s all just too good. I really like this version of pumpkin muffins because they are made with whole wheat flour that provides fiber and heartiness but are also filled with chocolate chips making them perfectly sweet too.

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Whole Wheat Pumpkin Muffins

I don’t exactly know why but kids seem to love anything that comes in the form of muffins. I think it’s the individual serving size and the fact that they look like cupcakes. You will feel good feeding your family these muffins because they a delicious and packed with vegetable, whole grains, and fiber.

Muffins make a great grab and go breakfast for busy mornings. If I want to make the meal more complete I’ll simply cook up some eggs and serve fruit with these pumpkin muffins too. These whole wheat pumpkin muffins also make a healthy snack that will actually fill you or your kids up instead of them asking for another snack 20 minutes later. 

Can pumpkin muffins be frozen?

Pumpkin muffins are the perfect thing to freeze. First, bake and cool the muffins completely, then put them in an airtight container and place in the freezer. They freeze very well. I’ll often throw frozen muffins in out lunch boxes and they are perfect for lunch.

How should I mix pumpkin muffins?

These muffins can easily be made stirring by hand. You want to gently stir the ingredients until they are just combined. Over-mixing will result in a tough muffin and we don’t want that! No knead to get out a mixer, just a plain old wooden spoon will work great.

Should I let the muffins cool in the pan before removing them? 

After I take my pumpkin muffins out of the oven, I let them cool in the pan for about 5 minutes. This will help the muffins hold their shape and not fall apart. Worth the wait! But don’t wait too long to take them out either or the bottoms start to get soggy from the steam.

More Muffin Recipes

If you’ve tried this whole wheat pumpkin muffin recipe or any other recipe on Bless this Mess, then don’t forget to rate the recipe and leave me a comment below! I would love to hear about your experience making it. And if you snapped some pictures of it, share it with me on Instagram so I can repost on my stories AND add your photo to your comment so that other can see your creation.

small pumpkin muffins on a cooling rack
5 from 1 vote

Whole Wheat Pumpkin Muffins

Light and fluffy pumpkin muffins made with 2 full cups of pumpkin puree (!!!), whole wheat flour, chocolate chips and not much else! Quick, easy, filling!
Prep: 5 minutes
Cook: 20 minutes
Total: 25 minutes
Servings: 12 -18 muffins


  • 1 can pumpkin puree, (15 ounce can), about 2 cups
  • 1 cup sugar
  • 2 eggs
  • 2 teaspoon vanilla extract
  • 2 cups whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon salt
  • 1 teaspoon cinnamon
  • 1 cup chocolate chips, divided
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  • Preheat the oven to 350 degrees F. and grease 2, 12-cup muffins tins well and set aside.
  • In a medium mixing bowl add the pumpkin puree, sugar, eggs, and vanilla. Mix well to combine.
  • Add the whole wheat flour, baking powder, salt, and cinnamon to the bowl.
  • Mix until well combined. 
  • Add 1/2 cup of the chocolate chips and stir to combine.
  • Add a scant 1/4 cup of batter to each cup in the the prepared muffin, it should make around 18 muffins.
  • Sprinkle the remaining 1/2 cup of chocolate chips over the top of the muffin batter. 
  • Bake for 20 minutes or until the muffins spring back when lightly touched.
  • Allow the muffins to cool for 2 minutes in the muffin tins and then remove them and allow them to cool on a wire rack. 
  • Serve warm or at room temperature. 
  • Store leftover muffins after they have full cooled in an airtight container for 3-4 days in the fridge or in the freezer for up to 3 months. 


  • This recipe is SUPER flexible! Add more chocolate chips if you’d like, omit the cinnamon, add more, or swap it for pumpkin pie spice if you’d like.
  • If you’d like to use honey in this recipe, reduce the amount to 3/4 of a cup bake the muffins at 325 degrees. It will take a few extra minutes to bake.
  • I’ve found if I’m using fresh ground wheat (that I ground at home) it takes an additional cup of flour for this recipe (I think the fresh ground wheat is just really airy and fluffy). 
  • I’m sure you could use a flax egg in this recipe to replace the eggs if you needed. 
  • If you want bigger muffins, you can fill the muffin cups up and cook them additional 5 of so minute, if you want quite small muffins (great for kids!) then you can distribute the muffins into 24 muffin cups and bake them for about 5 minutes less. You have flexibility on the size of muffin you make. You’ll know the muffin is done baking when it springs back when you lightly press the top. 


Serving: 1of 12 muffins, Calories: 220kcal, Carbohydrates: 41g, Protein: 4g, Fat: 6g, Saturated Fat: 3g, Polyunsaturated Fat: 0.4g, Monounsaturated Fat: 0.3g, Trans Fat: 0.003g, Cholesterol: 27mg, Sodium: 240mg, Potassium: 128mg, Fiber: 2g, Sugar: 25g, Vitamin A: 55IU, Vitamin C: 0.01mg, Calcium: 43mg, Iron: 1mg
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More pumpkin recipes:

Whole Wheat Pumpkin Muffins are good to make all year long. They are moist, full of fiber, and make a great breakfast or snack. Enjoy!

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