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, 1/3 cup coconut oil, 1/4 cup maple syrup (you can use honey or brown sugar if you’d like), 2 teaspoons of vanilla extract, 1 egg, 1 1/2 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!
5 from 2 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