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

freshly baked Pumpkin Oatmeal Muffins topped with nuts in a serving plate
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I have been enjoying Fall food wholeheartedly, first with the Chickpea Squash Fritters, then Butternut Squash SoupRoasted Pumpkin Soupcoconut 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 MuffinsWhole Wheat Carrot Chocolate Muffins, and Zucchini Chocolate Chip Muffins made from scratch. Check them out!

delicious whole wheat pumpkin oatmeal muffins on hand

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!

freshly milled flour in a white bowl using nutrimill

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.

ready to bake Pumpkin Oatmeal Muffins in a muffin molder

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

freshly baked Pumpkin Oatmeal Muffins in a muffin molder

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.
close up shot of Pumpkin Oatmeal Muffins sliced in half

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.

whole wheat pumpkin oatmeal muffins cut opened

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.

4.92 from 34 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

Equipment

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 teaspoon pumpkin pie spice 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, and wholesome recipes made using Instant Pot & Air Fryer, that are well tested, so you can cook with confidence.

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4.92 from 34 votes (24 ratings without comment)

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