Whole Wheat Pumpkin Muffins

These whole wheat pumpkin muffins are subtly sweet and moist. At only 160 calories apiece, they are the perfect lightened-up pumpkin dessert to have in your repertoire! They are a perfect addition to your breakfast when paired with a cup of coffee.

Thanksgiving is my favorite holiday, hands down. What’s so special about Thanksgiving, you’re probably asking yourself. In my opinion, it’s one of the few holidays that haven’t been ridiculously over-commercialized. You don’t need to buy presents or invest in overpriced decorations. The main focus of the day is time spent with those that you love. No matter who you are with, it’s a day that’s focused on camaraderie… and eating of course.

In preparation for Thanksgiving Day, I made these whole wheat pumpkin muffins in advance. I thought that popping these treats into the microwave for breakfast would be a quick and light treat for the morning, still leaving plenty of space for Thanksgiving dinner.

Why This Recipe Works

I like these muffins because they aren't overly sweet. They almost taste like a lightly sweetened biscuit. When paired with coffee or tea for breakfast, you've got a winning combination. This recipe has plenty of cinnamon, nutmeg, and ginger which gives the muffins a cozy pumpkin pie spice flavor. The whole wheat flour is a healthier substitution that should leave you satisfied afterward. My zucchini applesauce muffins are another healthy muffin recipe you'll want to check out!

Key Ingredients and Why We Use Them

• Whole Wheat Flour: Muffins and bread made with whole wheat flour are not as light as those made with regular unbleached all-purpose flour. These muffins indeed have more of a hearty feel to them, thanks to the whole wheat flour.
• Cinnamon + Nutmeg + Ginger + Cloves + Allspice: This combination of spices is also marketed as pumpkin pie spice. I like to buy the ingredients separately to use them interchangeably and don't risk one big bottle of pumpkin pie spice going unused.
• Brown Sugar: There is only ½ cup of lightly packed brown sugar in this recipe—not much at all. Just enough to help the muffins stay moist and tender.
• Pumpkin Puree: Be sure not to use pumpkin pie filling for these muffins. The pumpkin puree adds much-needed moisture to these muffins.
• Unsalted Butter: Melt your butter and then allow it to cool slightly before mixing with the sugar and other wet ingredients. Do not substitute butter in this recipe. It's needed to tenderize the batter and add flavor.
• Milk: Feel free to use any milk in this recipe. I almost always use whole milk when baking. Here are some great whole milk substitutions.

Use Two Temperatures to Cook Your Muffins

You know those tall and rounded muffins you see at your local bakery? There's a secret to achieving those perfect looking domes. Start high, and then go low. Are you with me? Start at a high temperature (usually 425) for about 5 minutes. Then reduce the temperature (the normal 350) for the remainder of the baking time. This allows you to get an initial shot of heat to puff up your muffins and then reduce the temperature to promote even cooking.

Whole Wheat Muffin Recipe Variations

There are many different ways to switch up this recipe according to your tastes. Here are some fun ideas to try!

• You can also use white whole wheat flour or all-purpose flour in the recipe. You can even get creative and try a mixture of whole wheat and all-purpose.
• Add ½ cup chopped pecans or walnuts to the batter.
• Try topping these muffins with a strudel mixture for some added sweetness.
• Want these muffins to be more dessert-like? Add 1 cup of chocolate chips to the batter!

Step by Step: How to Make these Muffins:

The entire recipe is below and be printed to save for later. Before you get there, let's walk through it step-by-step, so you understand what you're doing beforehand.

1. In a large bowl, whisk together flour, baking powder, baking soda, salt, and spices.

2. In a medium bowl, whisk the wet ingredients and sugar together (eggs, brown sugar, pumpkin puree, butter, vanilla, and milk).

3. Pour the wet ingredients into the dry and mix until just combined. Your batter can have a few streaks of flour—be careful not to overmix at this stage. The batter will be very thick.

4. Fill your muffin cups about ¾ full. Sprinkle with turbinado sugar, if desired.

Heather's Helpful Hints

• If some muffin cups remain empty during baking, put 2 to 3 tablespoons of water in the unused muffin cups to keep the pan from warping. I always like this tip for when my batter isn't quite enough for 12 muffins.
• Never make your muffin batter in advance. Your baking soda/powder becomes activated when you mix them with your wet ingredients. Waiting too long after this may cause your muffins not to rise fully. You could mix your dry ingredients in advance to save some time in advance.
• Set your stand mixer aside for muffins! You should stir the dry ingredients into the wet just until they are incorporated. We're talking 10 turns of a mixing spoon—maximum. Lumps and a few streaks of flour and totally acceptable.
• Similar to storing cupcakes, these muffins will last at room temperature for about three days before you want to eat or freeze them.

This recipe was originally posted in November 2012. It was updated in January 2021 with new pictures and a few updates to the recipe

Tell me How the Recipe Worked for YOU!

Did you make this recipe? First, let me say THANK YOU for giving it a try! Please leave us a rating above and leave any feedback in the comments section at the bottom of this post. I always love to hear your thoughts and ideas on what went well — and what didn’t — with a recipe! Be sure to check out some of our other recipes linked below!