Recipes > Breakfast > Healthy Pumpkin Banana Muffins

Healthy Pumpkin Banana Muffins

three healthy pumpkin banana muffins on a plate with a pan of muffins and a yellow coffee cup in the background

This is a variation of our whole wheat muffins base recipe. Pumpkin is the taste of fall, but by using canned pumpkin, you can make these muffins all year round! Packed with fresh fruit and veggies, whole grains, nuts, and a touch of spice, these healthy pumpkin banana muffins are going to become a staple in your house!

Three Must Know Cooking Skills

For recipe success, learn how to:

Culinary Tips for the Best Healthy Pumpkin Banana Muffins

Measure the flour properly to prevent dense muffins. Fluff, spoon, and level; don’t scoop and pack! 

Whisking the dry ingredients together mimics sifting and evenly distributes the ingredients, so don’t substitute another utensil.

If your bananas aren’t quite ripe enough, roast them! This takes just a few minutes and will quickly sweeten the bananas to improve the taste and texture of the muffins.

Add the toasted chopped pecans after whisking the dry ingredients to ensure even distribution.

Add pumpkin puree with the liquid ingredients. Be sure to use 100% pure pumpkin and not pumpkin pie filling.

When measuring brown sugar, pack it in the cup. If you are trying to reduce your sugar consumption or prefer less sweet muffins, reduce the sugar to ⅓ cup; the recipe will still come out great!

Don’t overmix the batter! Watch our muffin method culinary technique video to learn how to mix the batter just enough so that you end up with light and fluffy muffins.

Use a portion scoop to distribute the batter into the muffin tins. This handy tool can help make perfect muffins, cupcakes, pancakes, and more. It also makes the work easier; just squeeze the handle, and the batter slides right out!

We used a dark non-stick muffin pan to bake these muffins. If you use a light colored pan, the cooking time will increase.

To check for doneness, insert a toothpick into a muffin in the middle of the pan. If it comes out clean, it’s done! 

Ingredient Substitutions

  • White Whole Wheat Flour: substitute whole wheat pastry flour or spelt flour for a similar taste, color, and texture. You can also substitute 1 cup whole wheat flour and ½ cup all-purpose flour. We don’t recommend subbing all regular whole wheat flour, as the muffins will come out dense and grainy. To make gluten-free pumpkin muffins, use a gluten-free flour mix, such as Bob’s Red Mill 1-to-1 Gluten-Free Flour.
  • Cinnamon: substitute pumpkin pie or apple pie spice.
  • Kosher Salt: We use Morton kosher salt. If using Diamond Crystal kosher salt, use ¾  teaspoon. If you use table salt, use slightly less than ½ teaspoon. 
  • Pecans: substitute walnuts or pumpkin seeds, as these are classic pumpkin pairings, or substitute chopped, sliced, or slivered almonds or pistachios.
  • Pumpkin: substitute mashed or canned sweet potato or butternut squash.
  • Buttermilk: substitute plain yogurt, Greek yogurt, kefir, or sour cream. You can also make your own buttermilk by mixing ½ cup milk or milk alternative with ½ Tablespoon white vinegar or lemon juice.
  • Brown Sugar: substitute cane sugar, but note that the flavor will be slightly different. 
  • Canola Oil: substitute avocado oil. Do not substitute olive oil, as this has a strong flavor. Do not substitute vegetable oil, as this is not a heart-healthy oil. 
  • Eggs: to make vegan pumpkin banana muffins, substitute the eggs with flax eggs. To make two flax eggs, mix 2 Tablespoons of ground flaxseeds with 6 Tablespoons of water and let it rest for 10 minutes. Eggs help leaven the muffins, so a vegan version might not be quite as fluffy.

Recipe Variations

To make pumpkin banana chocolate chip muffins, add ½ cup chocolate chips. Note that adding chocolate chips may increase the yield, so bake extra batter in silicone liners.

Add 1 teaspoon of vanilla for an extra warming flavor.

Want to make mini muffins? Prepare a mini muffin pan with liners or non-stick spray and bake for 10-12 minutes, or until a toothpick inserted comes out clean.

This batter works for quick bread too! To make whole wheat quick bread, prepare a 9×5 loaf pan with parchment paper or non-stick spray. Cook for 50-55 minutes, or until a toothpick inserted into the middle comes out clean. 

Want more muffin recipe inspiration?

Use our base recipe as a guide to make it your own, or try these tasty variations!

Equipment Recommendations

Use these kitchen tools for recipe success:

Find all of our favorite kitchen tools here!

Are these Pumpkin Banana Muffins Healthy?

Yes! We wouldn’t use healthy in the title if they weren’t! Many pre-made muffins or store bought mixes contain way too much added sugar. Some even contain up to or even more than your daily allowance of sugar – yikes!

The key ingredients that make this scratch muffin recipe healthier than store bought varieties are whole wheat flour, banana, pumpkin, and less sugar than leading brands.

Whole Wheat Flour

Whole wheat flour is a good source of fiber, B vitamins, Vitamin E, trace minerals, and phytonutrients. Replacing refined grains (i.e. white flour) with whole grains (i.e. whole wheat flour) may reduce the risk of developing chronic conditions such as heart disease, diabetes, and certain types of cancer.


Bananas contain prebiotic fiber, vitamins, and minerals – important for digestion, energy, and metabolism. Greenish bananas are firm and are higher in prebiotic fiber. Brownish bananas are soft and are higher in sugar, making them a bit sweeter. By making this muffin recipe with bananas, you get natural sweetness from bananas, plus many other important nutrients!


Pumpkin is a great source of beta carotene, fiber, and potassium. These nutrients promote immune function, gut health, good cholesterol, and normal blood pressure. Be sure to purchase pure pumpkin puree and not canned pumpkin pie filling, as this contains added sugar.

Less Added Sugar

High sugar consumption is not good for health, and in general, most Americans eat way too much. Men should aim to consume less than 9 teaspoons (~36 grams) of sugar per day, and women should aim to consume less than 6 teaspoons (~24 grams) of sugar per day. Each muffin in this recipe has ~2 teaspoons (8 grams) of added sugar. 

Learn more about health benefits of different foods and ingredients in our book, To Your Taste!

Serving Suggestions for Pumpkin Banana Muffins

We doubt you’ll be able to resist biting into a warm, fluffy muffin when it’s fresh out of the oven! Enjoy on its own for a satisfying snack or dessert, topped with almond butter for a balanced breakfast, or as a sweet addition to lunch.

Storage Tips for Homemade Muffins

Because these are moist muffins, they will spoil more quickly at room temperature. Cool completely, then store the muffins in a bag or airtight container at room temperature for a few days or in the refrigerator for up to one week.

Got a busy few weeks ahead? These muffins are great for the freezer! Cool completely, wrap individually or in pairs, then store in a freezer-safe bag for up to 3 months. When ready to eat, thaw overnight in the refrigerator, or reheat in the microwave in the morning!

Want more pumpkin recipes to use up the rest of the can?

Try out these favorites, and as always, adjust to YOUR taste!

Pumpkin Oatmeal with Toasted Pumpkin Seeds

Pumpkin Energy Bites with Chocolate Chips

Whole Wheat Pumpkin Pancakes

Pumpkin Pie Overnight Oats

three healthy pumpkin banana muffins on a plate with a pan of muffins and a yellow coffee cup in the background

Healthy Pumpkin Banana Muffins

This is a variation of our whole wheat muffins base recipe. Packed with fresh fruit and veggies, whole grains, nuts, and a touch of spice, these healthy pumpkin banana muffins are going to become a staple in your house!
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast, Snack
Cuisine American
Servings 12 muffins


  • 1 ½ cups white whole wheat flour*
  • 1 teaspoon cinnamon
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon kosher salt
  • ½ cup chopped toasted pecans
  • 1 large very ripe banana (~½ cup mashed)
  • ½ cup pumpkin puree
  • ½ cup buttermilk
  • ½ cup packed brown sugar
  • ¼ cup canola oil
  • 2 large eggs


  • Preheat oven to 350°F. Prepare a 12-cup muffin pan with nonstick spray or muffin liners.
  • In a large bowl, gently whisk flour, cinnamon, baking powder, baking soda, and salt. Add pecans to flour mixture. Toss to evenly coat.
  • In a separate medium bowl, mash the banana. Add the pumpkin, buttermilk, brown sugar, oil, and eggs. Whisk to combine.
  • Add liquid ingredients to flour mixture. Using a spatula, fold ingredients just until moistened. Do not overmix.
  • Use a ¼ cup portion scoop to divide out the batter. Cook for 18-20 minutes, or until a toothpick inserted comes out clean. Enjoy!


*Substitute 1 cup whole wheat flour + ½ cup all purpose flour or 1 ½ cups whole wheat pastry flour.
Keyword Healthy Pumpkin Banana Muffins

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