Healthy Pumpkin Bran Muffins

The best healthy pumpkin bran muffins are low in fat and sugar, plus packed full of protein and essential vitamins & nutrients!

These pumpkin bran muffins check two of our favorite boxes – healthy and delicious. To keep that healthy streak going, try Healthy Breakfast Fruit Pizza, Healthy Zucchini Bread, and Healthy Whole Wheat Bran Muffins. They are sure to be a hit in your home too!  

Pumpkin Bran Muffins with cream cheese folded in

Healthy, but still delicious!

Lately we’ve been trying to focus on eating wholesome food, and that’s where these pumpkin bran muffins come in. They’re packed full of nutritious ingredients, ones that will help get your day off to a good start!

So what’s inside?

Pumpkin puree (aka lots of Vitamin A and fiber), Greek yogurt (protein), wheat bran (this stuff is gold people! b-complex vitamins and iron galore), and flaxseed meal (optional but loaded with micronutrients, fiber, manganese, vitamin B1, and omega-3).

So much goodness packed into these little muffins!!!

The best part is that you only need ONE bowl to make these in! Yes, just one bowl. Also, you can add anything you’d like to the batter to jazz these pumpkin bran muffins up. I sprinkled some raw pumpkin seeds on top and then swirled a bit of low-fat cream cheese into the rest.

Chunks of dark chocolate, pecans or cranberries would be amazing too! Enjoy & happy fall!

Healthy Pumpkin Bran Muffins with pumpkin seeds on top

Just mix, bake & enjoy

PREP. Preheat oven to 425 degrees. Lightly spray or line one muffin tin, set aside.

WET INGREDIENTS. In a small glass measuring cup or bowl, whisk together the pumpkin puree, yogurt, egg, oil, brown sugar, and vanilla.

DRY INGREDIENTS. In a separate mixing bowl whisk together the bran, flour, flaxseed meal, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Gradually pour in the wet ingredients into the bowl of dry ingredients along with any “mix-ins” (or reserve for the top), folding/mixing just until you see just a bit of dry ingredients (about 17-20 strokes).

Note. Be extra gentle with the batter. Folding in the dry ingredients just until a few dry patches remain (no more than 20 strokes with a big spatula) will help ensure that these come out tender and moist. Of course baking them to perfection is a big part of that too. Check them at the 12 minute mark. If the tops are set, pull them out right away!

BAKE. Scoop the batter into the prepared pan, dividing evenly between the wells. If you are using pepitas, sprinkle on the tops or if you are using cream cheese, place a teaspoon on top of each muffin and use a knife to gently fold in.

Place pumpkin bran muffins in the oven and bake for 12-14 minutes or until the tops are golden brown and spring back when touched. Remove from the oven and allow to cool in the pans for 5 minutes before transferring to a wire rack to cool completely.

Low Calorie Pumpkin Bran Muffins

Tips + SToring Info

  • Making your own Homemade Pumpkin Puree is fun and easy and would be amazing in this recipe!
  • Make sure that the coconut oil you use in this recipe is melted and not solid when you are adding it.
  • To make 6 jumbo muffins with this recipe just adjust the baking time to about 17-20 min checking to see when the tops are golden brown and spring back when touched to be sure they are done.

STORE covered pumpkin bran muffins on the counter top for a few days. They are best stored tightly covered and refrigerated. 

FREEZE any leftover muffins, just make sure they have cooled completely before you do so. We suggest either storing them in a Ziploc freezer bag or wrapping them tightly in plastic wrap followed by aluminum foil.  These muffins can be frozen for up to 3 months and then thawed at room temperature or warmed in the microwave when you are ready to enjoy them later.

Healthy Pumpkin Bran Muffins with pumpkin seeds on top

More great muffin recipes that are quick and oh so delicious:

Healthy Pumpkin Bran Muffins

Healthy Pumpkin Bran Muffins Recipe

The best healthy pumpkin bran muffins are low in fat and sugar, plus packed full of protein and essential vitamins & nutrients!
4.69 from 16 votes
Pin Rate
Course: Breads & Muffins
Cuisine: American
Prep Time: 5 mins
Cook Time: 12 mins
Total Time: 17 mins
Servings: 12 muffins
Calories: 162kcal
Print Recipe

Ingredients

  • 1 cup pumpkin puree - not pie filling
  • 2/3 cup Greek yogurt
  • 1 egg
  • 1/3 cup coconut oil
  • 1/4-1/3 cup maple syrup - OR honey OR brown sugar*
  • 2 tsp vanilla extract
  • 1 1/2 cup wheat bran
  • 1 cup whole wheat flour**
  • 1 tbsp golden flaxseed meal
  • 1 1/2 tsp baking powder
  • 1 1/2 tsp baking soda
  • 1/4 tsp salt
  • 2 tsp ground cinnamon
  • 1/4 tsp ground ginger
  • 1/4 tsp ground nutmeg
  • 1/8 tsp ground cloves
  • 1/2 cup pumpkin seeds - (pepitas), chopped nuts, bittersweet chocolate chips, dried fruit or ⅓ the fat cream cheese

Instructions

  • Preheat oven to 425 degrees. Lightly spray or line one muffin tin, set aside.
  • In a small glass measuring cup or bowl, whisk together the pumpkin puree, yogurt, egg, oil, brown sugar, and vanilla.
  • In a separate mixing bowl whisk together the bran, flour, flaxseed meal, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Gradually pour in the wet ingredients into the bowl of dry ingredients along with any "mix-ins" (or reserve for the top), folding/mixing just until you see just a bit of dry ingredients (about 17-20 strokes).
  • Scoop the batter into the prepared pan, dividing evenly between the wells. If you are using pepitas, sprinkle on the tops or if you are using cream cheese, place an teaspoon on top of each muffin and use a knife to gently fold in. Place in the oven and bake for 12-14 minutes or until the tops are golden brown and spring back when touched. Remove from the oven and allow to cool in the pans for 5 minutes before transferring to a wire rack to cool completely.

Notes

*If you like your muffins on the sweeter side, use the full ⅓ cup of sweetener.
**You can use only whole-wheat flour, only all-purpose flour, or a ½ c. whole-wheat flour + ½ c. all-purpose flour. They taste great no matter what you use!

Nutrition

Serving: 12g | Calories: 162kcal | Carbohydrates: 20g | Protein: 5g | Fat: 9g | Saturated Fat: 6g | Cholesterol: 14mg | Sodium: 218mg | Potassium: 292mg | Fiber: 5g | Sugar: 5g | Vitamin A: 3197IU | Vitamin C: 1mg | Calcium: 70mg | Iron: 2mg

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Comments:

  1. These were very very good. Got worried the batter was so thick but it came out moist and airy enough and just lovely.

  2. Not too sweet. Pillowy soft. Love all the nutrition packed in these. Also a fan of the flexibility of some of the ingredients, like the flours. Made half the batch with walnuts and raisins; the other half had chocolate chips. Our family even has different ideas about “sweet” so I stirred up some honey butter for the bigger sweet tooths of the family. 

  3. Can I use coconut sugar? Also, if I double can I add 1/4 other flour such as oat, one more ? 
    Should I melt coconut oil? Thanks for recipe 

    1. Hi Pamela, I haven’t tried using coconut sugar or adding another type of flour. The coconut oil should be melted.

  4. I used your recipe and made vegan swaps and they were amazing!!
    I subbed silken tofu for yogurt
    I used the brown sugar option
    I used flax eggs (1 TBSP of ground flax + 1 1/2 tbsps of water for each “egg”)
    I didn’t add the extra flax since I already used the flax egg.
    Thanks for the great post. ?

  5. 5 stars
    Excellent! With the pandemic, I am staying home, trying to find healthy recipes WITH ingredients I have on hand (since grocery store are wiped out of flour, etc). I substituted 1/2 oat bran flour & 1/2 whole wheat pastry flour, & a bit of grass fed butter with the coconut oil and baked in a silicone mini bar mold that fits in our Breville toaster oven – they turned out GREAT! Thank you! Stay safe, Healthy!

    1. You are so welcome! I am glad you found this recipe. Thank you for sharing what you did 🙂

  6. What’s the difference between wheat bran and oat bran? Can that be subbed in the same ratio? It looks like a great recipe, can’t wait to try it.

    1. We love these! I hope you try them! Wheat bran has a higher quantity of fiber, but yes, you can use either 🙂

  7. 5 stars
    Love this recipe and can’t wait to try! Question on the cream cheese you folded in at the end – did you warm the cream cheese to room temperature so it was easier to fold in? Thanks.

  8. What would be a substitute for flaxseed meal in this recipe? An extra egg, almond meal, chia seeds, or more yogurt?
    Thx in advance.

    1. That’s a good question. I have not personally substituted that, so my best bet would be to google what good substitutions would be for the flaxseed.

      1. Since my google attempt already provided the above options, I guess the better way to ask the question you is what purpose does the flax seed meal provide in the recipe you created? Binding agent vs fiber vs nutrition value? I’ll pick my substitute accordingly. Thx.

  9. 5 stars
    Best ever pumpkin bran muffins! I added plumped up raisins and made 6 jumbo muffins. The baking time took about 20 minutes. Very moist and delicious! Thank you!

  10. 5 stars
    I have now made this recipe 3 times all with slight variations.
    The first time was as the recipe was written.
    Second time. I added frozen apple chunks. I chopped them in small cubes, mixed into flour mixture before adding wet ingredients. I used butternut squash instead of pumpkin
    Today, used butternut squash, appplesauce for half the oil, molasses for the sweetener, raisins and apples. This recipe is perfect for variations.
    All three times the muffins were perfect.

  11. 5 stars
    You wouldn’t know that these were healthy. So much flavor and the texture is perfect too! This is something I won’t feel guilty about snacking on!

  12. 5 stars
    Thanks a lot for this pumpkin bran muffins recipe! So easy to make and tasted really delicious! Fam loves it, will have it again! Highly recommended!