Start your day right with these Healthy Pumpkin Bran Muffins! Low in fat, sugar-free, yet rich in protein and vital nutrients!

This Healthy Pumpkin Bran Muffins Recipe is the perfect start to your day! They are packed with vitamins and nutrients and taste delicious! Plus, these bran pumpkin muffins are so versatile and you can really make them your own. I swirled in some low fat cream cheese into come and added pumpkin seeds on top to others.
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!
Table of Contents
Reasons to Love These Healthy Bran Muffins
- These Pumpkin Bran Muffins are packed with essential nutrients.
- Bran muffins are versatile. You can customize it with fruits, nuts, or spices.
- These muffins are a quick, convenient breakfast or snack option.
Recipe Ingredients

- Pumpkin Puree: Pumpkin Puree adds a creamy texture and rich, earthy sweetness.
- Ground Cinnamon: Offers a warm, spicy note that is quintessential in pumpkin recipes.
- Greek Yogurt: Adds creaminess and tang and helps to tenderize the muffins.
See the recipe card for full information on ingredients and quantities.
Variations
- Spice Variations: For a seasonal twist, consider adding pumpkin pie spice or allspice to your muffins. These spices bring warm, aromatic flavors that evoke the essence of autumn and complement a variety of muffin recipes. A dash of pumpkin pie spice or allspice will infuse your baked goods with a cozy, comforting taste.
- Topping Options: Sprinkle coarse sugar for a sweet crunch, add chopped nuts for texture, or fruit and raisins for a burst of flavor. A streusel topping can also offer a decadent, crumbly finish.
How to Make Healthy Pumpkin Bran Muffins
Step 1: Preheat oven to 425 degrees Fahrenheit (218 degrees Celsius). Lightly spray or line one muffin tin, and set aside.
Step 2: In a small glass measuring cup or bowl, whisk together the pumpkin puree, yogurt, egg, oil, brown sugar, and vanilla.
Step 3: In a separate mixing bowl, whisk together the bran, flour, flaxseed meal, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves. Gradually pour 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).
Step 4: Scoop the batter into the prepared pan, dividing evenly between the wells. If you are using pepitas, sprinkle them 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 it 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.

Expert Tips
- Puree Perfection: Making your own Homemade Pumpkin Puree is fun and easy and would be amazing in this recipe!
- Even Baking: Fill each muffin well evenly using an ice cream scoop or a large spoon. This promotes uniform cooking and perfectly shaped muffins.
- Oil Consistency: Make sure that the coconut oil you use in this recipe is melted and not solid when you are adding it.

Frequently Asked Questions
Yes, you can make 6 jumbo muffins using this recipe. Simply adjust the baking time to about 17-20 minutes, checking periodically. Ensure they are fully baked once the tops are golden brown and spring back when touched.
Insert a toothpick into the center of a muffin. If it comes out clean or with a few moist crumbs attached, the muffins are done baking.
Storage Info
STORE these Healthy Pumpkin Bran Muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to a week. To FREEZE, store them in your freezer in a sealed bag or wrap them tightly in plastic wrap followed by aluminum foil for up to 3 months.
To REHEAT, thaw if frozen, and warm in a microwave for about 20-30 seconds or in an oven preheated to 350 degrees Fahrenheit (175 degrees Celsius) for 5-10 minutes until heated through.
More Delicious Muffin Recipes You’ll Love

Healthy Pumpkin Bran Muffins 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 Fahrenheit (218 degrees Celsius). Lightly spray or line one muffin tin, and 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 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 them 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 it 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.











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!
Great idea!! Glad you liked them! Thank you for letting me know 🙂
What would be a substitute for flaxseed meal in this recipe? An extra egg, almond meal, chia seeds, or more yogurt?
Thx in advance.
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.
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.
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.
I hope you like it! Yes, room temp will make it easier 🙂 Enjoy!
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.
We love these! I hope you try them! Wheat bran has a higher quantity of fiber, but yes, you can use either 🙂
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!
You are so welcome! I am glad you found this recipe. Thank you for sharing what you did 🙂