Healthy Pumpkin Bran Muffins

It’s officially fall! That means the more pumpkin, the merrier! ???????? During the past few weeks I’ve been working on turning my favorite bran muffin into a spiced pumpkin version. Today I’m sharing the result of 3 trial batches and a whole lot of taste testing 🙂

Healthy Pumpkin Bran Muffins

Lately we’ve been trying to focus on feeding our toddler healthy, wholesome food. While we’ve done a pretty good job, I feel like ever since baby #2 was born, things have become a little too relaxed. That’s where these golden beauties come in. They’re packed full of nutritious ingredients, ones that will help get your day off to a good start!

Healthy Pumpkin Bran Muffins

So what’s inside? 1 cup of pumpkin puree (aka lots of Vitamin A and fiber), 2/3 cup of Greek yogurt (protien!)… I used Chobani’s blended pumpkin spice and it was a match made in heaven, ⅓ cup coconut oil, ¼ cup maple syrup (you can use honey or brown sugar if you’d like), 2 teaspoons of vanilla extract, 1 egg, 1 ½ cup of wheat bran (this stuff is gold people! b-complex vitamins and iron galore), 1 cup of white whole wheat flour (it’s more mild and not as noticeable), 1 tbsp. of flaxseed meal (optional but loaded with micronutrients, fiber, manganese, vitamin B1, and omega-3), baking powder, baking soda, salt, lots of cinnamon and spices like ginger, nutmeg and cloves. So much goodness packed into these little muffins!!!

Healthy Pumpkin Bran Muffins

The best part is that you only need ONE bowl to make these in! Yes, just one bowl ????. Just 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!

Healthy Pumpkin Bran Muffins

P.S. you can add anything you’d like to the batter to jazz these up. I sprinkled some raw pumpkin seeds on top and then swirled a bit of low-fat cream cheese into the rest. But chunks of dark chocolate, pecans or cranberries would be amazing too! Enjoy & happy fall!

Healthy Pumpkin Bran Muffins

Healthy Pumpkin Bran Muffins Recipe

These are the best healthy pumpkin bran muffins out there! Not only are they low in fat, but they're low in sugar too. Plus they're packed full of protein along with essential vitamins & nutrients!
4.88 from 8 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


  • 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 1/3 the fat cream cheese


  • 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.


*If you like your muffins on the sweeter side, use the full 1/3 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!


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

Like this Recipe?

Pin it now!

Pin It Now0Pin It Now0

Shop Online

Lil' Luna Products

See All Products

Want more inspiration?

More Recipes You'll Love

Roasted Salsa Verde

Total Time: 20 minutes
5 from 4 votes

Beef Enchiladas

Total Time: 2 hours 30 minutes
5 from 2 votes

Mini Lemon Cheesecakes

Total Time: 50 minutes
5 from 3 votes

Lemon Cream Pie

Total Time: 4 hours 42 minutes
4.69 from 19 votes

About the Author


Wife, mother, baker and photographer. Recipe developer & author of Life Made Simple. A self-professed peanut butter lover and fond of anything that involves pumpkin, cookie dough, or sprinkles

Join the Conversation

Rate and Comment

Your email address will not be published. Required fields are marked *

Recipe Rating

This site uses Akismet to reduce spam. Learn how your comment data is processed.


  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.