I have been enjoying Fall food wholeheartedly, first with the Chickpea Squash Fritters, then Butternut Squash Soup, Roasted Pumpkin Soup, coconut pumpkin halwa, and now these Healthy Whole Wheat Pumpkin Muffins. I have made many muffins (adding chocolate chips to all) because my daughter loves them. But I also want to make them healthier so she does not get empty calories. Hence, this recipe comes to you with wonderful ingredients that you will not mind enjoying any time with your cup of warm coffee or tea. You might also like these Almond Flour Pumpkin Muffins, Whole Wheat Carrot Chocolate Muffins, and Zucchini Chocolate Chip Muffins made from scratch. Check them out! I have been making homemade pumpkin puree in my Instant Pot. Try it now if you have not. It is so easy. However, with that, I need lots of ways to use the pumpkin puree. Hence, this pumpkin oatmeal muffin recipe is an easy way to use. I also recently got the Nutrimill, an excellent machine for freshly milled flour. And I must say I am so impressed with the softness of the muffins with the fresh flour. It takes just 2 minutes to start the Nutrimill and get freshly milled whole wheat flour. It is like magic!

Easy step-by-step recipe for Whole Wheat Pumpkin Muffins

Start with pre-heating the oven to 350F. Line a 12-count muffin tray with liners. First, we will mix the dry ingredients in a large bowl: whole wheat flour, rolled oats, baking soda, baking powder, ground cinnamon, nutmeg, cloves, and salt. Mix them well and set them aside. Mix the wet ingredients in a separate bowl. Whisk the eggs and brown sugar, then add pumpkin puree, melted butter, vanilla, and yogurt. Mix well until combined. Mix the dry ingredients into the wet ingredients bowl. Add the chocolate chips and fold everything together gently until combined. Scoop batter into the prepared muffin tray, filling each cup but leaving some space for the muffins to fluff. Sprinkle with pumpkin seeds and rolled oats. Bake for about 18-20 minutes or until the toothpick inserted in the center of a muffin comes out clean. Don’t they look gorgeous?  I have cut one below to show you how soft they were for whole wheat muffins.

Tips to make the Best Healthy Pumpkin Muffins

Chocolate chips are optional. You can skip them from this recipe or replace them with walnuts or cranberries. I used brown sugar, but maple syrup can also be used to sweeten these muffins. I added rolled oats to this recipe. However, they can be skipped without any change to the recipe. These muffins can be refrigerated for up to 4 days. Let them cool on a wire rack before saving them in an airtight container. I lightly warm them in the microwave for 10 seconds before enjoying them. You can also freeze them in a freezer-safe container or ziplock bag for up to 4 months.

Sometimes, I enjoy topping them with sugar glaze to give them a sweet kick (okay, am I making them a bit unhealthy here?).

Why you will love these Whole Wheat Pumpkin Muffins?

√ Make with freshly milled whole wheat flour and oats, so they are super healthy √ They are so soft and perfect with your warm cup of tea or coffee √ Great snack for kids with all the healthy ingredients √ Easy to customize – include or skip chocolate chips, add walnuts or cranberries √ They are freezer-friendly. Enjoy these healthy whole wheat muffins made with freshly milled flour. You can use store-bought whole wheat flour in this recipe. Here is a Fall appetizer where you can use Nutrimill to make freshly milled chickpea flour – Chickpea Squash Fritters.

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