Kickstart your Fall mornings with these Healthy Whole Wheat Pumpkin Oatmeal Muffins. Made with freshly milled whole wheat flour, rolled oats, pumpkin puree, yogurt, and chocolate chips, these satisfying goodies are guilt-free.
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.
If you want to get your hands on Nutrimill, here is my affiliate link Nutrimill Harvest. It is a great price and machine you don’t want to miss, especially if you enjoy baking. If you want to buy Nutrimill on Amazon, here is the link – Nutrimill Harvest.
Here is a Fall appetizer where you can use Nutrimill to make freshly milled chickpea flour – Chickpea Squash Fritters.
Healthy Whole Wheat Pumpkin Oatmeal Muffins Recipe
Equipment
Ingredients
- 1.5 cup Whole Wheat Flour, freshly milled in Nutrimill, 6.1 oz
- 1/2 cup Rolled Oats , 1.6 oz + more for garnish
- 1 teaspoon Baking Soda
- 1 teaspoon Baking powder
- 1 teaspoon Ground Cinnamon
- 1/3 teaspoon Ground Nutmeg
- 1/4 teaspoon Ground Cloves
- 1/4 teaspoon Salt
- 2 Eggs
- 1/2 cup Brown Sugar , lightly packed
- 1 cup Pumpkin Puree
- 1/3 cup Unsalted Butter
- 1 teaspoon Vanilla Extract
- 1/4 cup Plain Yogurt
- 1/2 cup Chocolate chips
- 2 tablespoon Pumpkin seeds
Instructions
- Preheat oven to 350 degrees F. Line a 12 muffin tray with cupcake liners.
- In a large bowl, mix together whole wheat flour, rolled oats, baking soda, baking powder, ground cinnamon, nutmeg, cloves and salt. Mix them well and set aside.
- In a separate bowl, start mixing the wet ingredients – whisk the eggs, brown sugar, then add pumpkin puree, melted butter, vanilla and yogurt. Mix all 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 prepared muffin tin, filling each cup but leaving some space for the muffins to fluff. Sprinkle with pumpkin seeds and rolled oats.
- Bake for about 20 minutes or until toothpick inserted in the center of muffin comes out clean.
- Remove baking try from the oven. Allow muffins to cool before enjoying.
What a nice, versatile recipe! I used 1/2 pumpkin and 1/2 applesauce, and chose walnuts instead of chocolate chips. They baked up light and fluffy, and just a little sweet – perfect! Quite wonderful compared to the super sweet white flour things we typically see. I’ll make these over and over, varying the add-ons. Thank you!
Hi Laurie – So glad you enjoyed the muffins. Thank you for sharing the changes you made 🙂
I made these and they were delicious! I’m just wondering if there is a way to keep the pumpkin seeds from falling off? Maybe an egg white wash before sprinkling?
Hi Melisa – I have not tried using an egg wash, but no reason why it wouldn’t work. Happy to hear you enjoyed the muffins.
Delicious! Whole family approved. Full of wholesome ingredients. I used my home milled hard red wheat flour and added some ground flax just for fun. Will make again for sure. Thank you!
Hi Jen – So good to hear that 🙂
I hardly think these are healthy when you use eggs and butter!
Kevin, there are multitudes of ideas about what’s healthy and what’s not. This recipe is 100% whole grains and uses WAY less sugar than typical muffins. You could make your own changes, oil (IF you consider THAT as healthy, which done do not), and use a flax egg substitute. To each his own.
Perfect recipe! Thank you! I used coconut oil instead of butter and walnuts instead of pumpkin seeds. Freezing these for when baby arrives and I need healthy options 🙂
I have probably used this recipe two dozen times in the past year, because it’s wonderful. I double the recipe in order to use one whole can of pumpkin purée (it’s not exact per the recipe, but close and turns out right). I also use part almond meal to replace some of the flour (for single recipe, mine is 1 c wheat flour, 1/2 c almond meal). It’s so tasty and comes out perfectly each time!
I made these this morning and they turned out perfect! I used 1/4 cup of honey instead of brown sugar to make them just a little more diabetic friendly for my husband and it worked great. Thank you for sharing the recipe!
What whole wheat grains did you use for milling the flour? Could you point to the right grains that I can buy in the US?
Hi Mounica – I used red wheat berries I got at Whole Foods to make the flour for this recipe. I could only fine wheat berries at Whole Foods, so that is what I used.
I want to make these vegan. If I skip the yogurt and butter will they turn out ok? So I need to sub something else? Thanks!
Hey Kari – I have not tried so it is hard for me to confirm it will work perfectly. My guess is to replace butter with your choice of vegetable oil and yogurt for vegan yogurt or soy/almond milk. Please do let me know if you try as it will help other readers. Thank you!