Kickstart your Fall mornings, which these Healthy Whole Wheat Pumpkin Oatmeal Muffins. Made with freshly milled whole wheat flour, rolled oats, pumpkin puree, yogurt along with chocolate chips, these are satisfying goodies that you can enjoy guilt free. 

Healthy Whole Wheat Pumpkin Muffins

I have been enjoying Fall food wholeheartedly, firstly with the Chickpea Squash Fritters, then Butternut Squash Soup, Roasted Pumpkin SoupCoconut Pumpkin Halwa, and now these Healthy Whole Wheat Pumpkin Muffins.

I have made many muffins (adding chocolate chips to all) as my daughter loves them. But I also want to make them healthier, so she is not getting just empty calories. Hence this recipe comes to you with all 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 MuffinsWhole Wheat Carrot Chocolate Muffins, and Zucchini Chocolate Chip Muffins made from scratch. Check them out!

Healthy pumpkin oatmeal muffins - closeup

I have been making homemade pumpkin puree in my instant pot. Try now if you have not tried. It is so easy. However, with that, I need lots of ways to use the pumpkin puree. Hence this Pumpkin Oatmeal Muffins recipe is one easy way to use it.

I also recently got the Nutrimill, a wonderful 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!

Nutrimill with freshly millled flour

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.

We will first 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 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 tray, filling each cup but leaving some space for the muffins to fluff. Sprinkle with pumpkin seeds and rolled oats.

whole wheat pumpkin muffins - ready to go in oven

Bake for about 18-20 minutes or until the toothpick inserted in the center of a muffin comes out clean.

whole wheat pumpkin muffins - ready in the baking tray

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 just 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 air-tight container in the refrigerator. I lightly warm them in the microwave for 10 seconds before enjoying them.
whole wheat pumpkin oatmeal muffins

Sometimes I enjoy topping them with some sugar glaze to get a sweet kick (okay, I am 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

whole wheat pumpkin muffins with Nutrimill

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.

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4.66 from 29 votes

Healthy Whole Wheat Pumpkin Oatmeal Muffins Recipe

Kickstart your Fall mornings, which these Healthy Whole Wheat Pumpkin Oatmeal Muffins. Made with freshly milled whole wheat flour, rolled oats, pumpkin puree, yogurt along with chocolate chips, these are moist satisfying goodies that you can enjoy guilt free. 
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 12 muffins

Ingredients 

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.

Notes

All-purpose flour: You can also use all-purpose flour in this recipe. Or a mix of whole wheat and all-purpose.
Pumpkin Spice blend: You can use 1 tsp pumpkin side blend in place of the nutmeg and cloves in this recipe. 
Chocolate chips: They are optional. You can add walnuts or cranberries to change up when making these muffins multiple times. 
Serving Options: Serve the muffins on their own, with a pat of butter, or spread some almond butter. 
Don’t like oats: You can simply skip them

Nutrition

Calories: 212kcalCarbohydrates: 29gProtein: 4gFat: 9gSaturated Fat: 4gCholesterol: 41mgSodium: 176mgPotassium: 194mgFiber: 3gSugar: 14gVitamin A: 3240IUVitamin C: 0.8mgCalcium: 61mgIron: 1.5mg

Additional Info

Course: Breakfast, Snack
Cuisine: American
Diet: Nut-free, Vegetarian
Tried this recipe?Mention @pipingpotcurry or tag #pipingpotcurry!

About Meeta

I strongly believe that each one of us has a chef inside us, we just need to explore the ingredients and create great food. My passion is to share easy, healthy, and wholesome recipes made using Instant Pot & Air Fryer, that are well tested, so you can cook with confidence.

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8 Comments

  1. 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 🙂

  2. 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!

  3. 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!

  4. 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?

    1. 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.

  5. 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!

    1. 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!