The Best Healthy Pumpkin Banana Muffins with Fall Spices

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These delicious & easy Pumpkin Banana Muffins are lower in sugar, baked with healthy whole grains, and rich with warm autumn spices. They’re sure to become a family favorite you make again and again! They are perfect for breakfast or an afternoon snack, and these muffins are only 150 calories a piece.

white plate of healthy pumpkin banana muffins stacked in a tower

Back when I was teaching full-time, fall was always the busiest season of the year. It was fun, new, and exciting, but so exhausting as I adjusted to a new teaching schedule and got back into the swing of things.

To get me through those long exhausting days, one of my favorite things to do was help myself to a baked treat with a mug of decaf coffee after the kids went home while I finished up some paperwork and answered emails. Eventually, it became so ritualized that even though I no longer teach full-time, I still fully need my afternoon snack with a coffee.

Pumpkin spice treats are some of my favorites–it is pumpkin season, after all. These scrumptiously spiced and deliciously moist pumpkin banana muffins are perfect for this time of year! They simply the best, especially now as I try to watch my sugar intake and increase fiber. Finding a way to still get in a little sweet treat without throwing myself off from my health goals is amazing!

These muffins have a deliciously rich pumpkin taste and light banana flavor.


For these healthy pumpkin banana muffins, you will use:

  • Whole Wheat Pastry Flour– Pastry flour is made from soft wheat (as opposed to hard wheat). That gives a more delicate texture for things like muffins and cakes. If you do not have pastry flour, you could sub in a lighter texture hard wheat, such as white whole wheat flour, in order to keep it whole grain. However, all-purpose flour could work, too.
  • Pumpkin Puree– Choose pumpkin puree, not pumpkin pie filling. You will use a whole 15-oz can!
  • Overripe Bananas– We will use two of them. The natural sweetness of the bananas enhances the muffin batter, which allows us to cut down on sugar. The addition of bananas and pumpkin puree also allows us to pull back on the amount of oil that would typically be used in a muffin recipe while still keeping them moist.
  • Sugar– I’m using organic cane sugar, which is why it has a slightly brown hue. Coconut sugar would also be a great choice. No brown sugar is needed in this recipe.
  • Eggs– 4 of them! We use a lot of eggs in this recipe, but it does make two and a half dozen muffins.
  • Avocado Oil– Just a small amount. I love avocado oil for it’s neutral taste and healthy fat profile. Olive oil or coconut oil could be subbed if you don’t mind the flavor either one imparts.
  • Baking Essentials & Warm Spices– Baking soda & baking powder, vanilla extract, salt, cinnamon, nutmeg, cloves, and ginger. You could sub pumpkin pie spice if you wish.
pumpkin banana muffin ingredients on dark wooden table


Follow the steps below to create these delicious & healthy pumpkin banana muffins:

oven panel reading 350 degrees

1. Preheat Oven

Preheat your oven to 350 degrees Fahrenheit.

adding baking spices to a bowl of flour

2. Whisk Flour & Spices

Measure the whole wheat pastry flour into a medium or large bowl (I like to use a scale–if using a measuring cup, spoon your flour into the cup to make sure you don’t pack them too full). Add the baking soda, baking powder, cinnamon, nutmeg, cloves, ginger, and salt. Whisk together until combined, then set aside.

stainless mixer bowl with banana chunks

3. Mash Banana

Peel your banana and break it into chunks. Add banana pieces to the bowl of your stand mixer and mix on medium speed until they are thoroughly mashed. Alternatively, you can mash these in a bowl with a potato masher or fork.

mixing bowl of pumpkin banana muffin batter

4. Add Wet Ingredients

Add your can of pumpkin and sugar to the bowl of mashed banana and stir together. Add your eggs one at a time, mixing in between each one. Add your vanilla extract, water, and avocado oil. Stir until smooth.

flour added to muffin batter in mixer

5. Add Dry Ingredients

Add your bowl of flour & spices to the mixing bowl. Stir until just combined.

filling muffin tin with batter

6. Fill Each Muffin Tin

Line three muffin tins with paper liners. Using a standard-sized cookie scoop, scoop two scoops of batter into the muffin cups. If you don’t have a scoop, fill each one 2/3 full.

adding chocolate tips on top of each muffin

7. Top with Chocolate

Top each muffin with 1 tsp mini chocolate chips.

muffin tin of pumpkin banana muffins

8. Bake

Bake muffins for 22-24 minutes or until a toothpick comes out clean when inserted. Let them cool in the muffin pan for 10 minutes, then remove the muffins and let them finish cooling on a wire rack. Enjoy!

Tips & Variations

If you would rather have the chocolate chips in the muffins instead of as a topping, you can fold in 1/2 cup + 2 tbsp chocolate chips to the batter after you finish mixing.

If you’re not a chocolate lover, you can leave the chocolate chips out. You could replace it with chopped walnuts–that would be amazing!

This recipe would also make awesome mini muffins! Use a cookie scoop and just do one scoop per muffin cup, then bake for 15-16 minutes or until the toothpick comes out clean.

Serving Suggestions

You an enjoy these muffins as soon as they’re cool enough to handle! They should last four to five days at room temperature in a sealed container.

Have a muffin with a cup of coffee in the mornings or as an afternoon snack. They are great just as they are, however, I’m partial to a little melted butter on mine.

Make sure you have some protein with it! Try them with our High Protein Overnight Oats, especially for a pre-workout carb boost!

plate of pumpkin banana muffins arranged in circle on plate

Nutritional Information

Per one muffin:

  • Calories: 155 (But they could be lower if you choose sugar-free chocolate chips, such as Lily’s Chocolate Chips)
  • Protein: 3.5 grams
  • Fat: 6.1 grams (1.6 grams saturated)
  • Carbs: 24.3 grams
  • Fiber: 2.4 grams

Recipe Notes & Other Suggestions

If you store these muffins at room temperature in an airtight container, they will last 4-5 days.

I love using cookie scoops to help me portion muffin batter because it’s much less messy than a spoon or trying to pour it. Scoops also measure the batter so that each muffin is evenly portioned, which helps them all bake evenly.

These muffins freeze well if you would like to store some of them away to eat at another time. Wrap individual muffins in plastic wrap or store several of them in a freezer bag with as much air removed as possible.

If you’re looking for some other fun seasonal recipes, try my Banana Carrot MuffinsCranberry Orange Sourdough or Cranberry Wild Rice Bread!

If you’re looking for a sweeter treat, try my Peanut Butter Blossom Cookie Bars, healthy oatmeal ginger molasses cookies, or protein cereal bars! You’ll also love my 3-ingredient Date Snickers.

Get Your Fall Baking On!

This is one of my family’s favorite pumpkin recipes. I’m sure your family will love it, too. If you give this recipe a try, please leave a comment and review! It means the world!

white plate of healthy pumpkin banana muffins stacked in a tower
Print Recipe
5 from 2 votes

Pumpkin Banana Muffins with Fall Spices

This delicious pumpkin banana muffin recipe is made with whole grains and reduced amounts of sugar to create a delcious, but healthy treat perfect for a mid-afternoon pick-me-up!
Prep Time10 minutes
Cook Time22 minutes
Total Time32 minutes
Course: Breakfast, Snack
Cuisine: American
Keyword: healthy pumpkin muffins, muffins, pumpkin, pumpkin banana muffins, whole grain muffins
Servings: 30
Calories: 155kcal
Author: Holly Lee
Cost: $5


  • 1 Cookie Scoop optional
  • Muffin Tins


  • 3 1/2 cups Whole Wheat Pastry Flour 420 grams
  • 2 tsp Baking Soda
  • 1 tsp Baking Powder
  • 1 tsp Ground Cinnamon
  • 1 tsp Ground Nutmeg
  • 1/2 tsp Ground Cloves
  • 1/4 tsp Ground Ginger
  • 1 1/2 tsp Salt
  • 2 Bananas overripe
  • 15 oz Pumpkin (1 can)
  • 1 1/4 cup Cane Sugar
  • 4 Eggs
  • 1 tsp Vanilla Extract
  • 1/2 cup Avocado Oil
  • 2/3 cup Water
  • 2/3 cup Mini Chocolate Chips


  • Into a medium mixing bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, cloves, ginger, and salt. Set aside.
  • Peel your overripe bananas and break them into a few pieces. Add them to the bowl of a stand mixer. Turn on your mixer and stir until the bananas are smoothly mashed. Turn off the mixer.
  • Add the rest of your wet ingredients to the stand mixer bowl, stirring the batter in between each addition. Add the can of pumpkin and sugar and mix. Then add your eggs one at a time, stirring after each addition. Then add water, vanilla, and avocado oil. Stir until smooth.
  • Gradually add your flour mixture to the wet ingredients and mix until it's evenly combined. Avoid overmixing.
  • Line a muffin tin with muffin wrappers. Fill each muffin wrapper about 2/3 full. If using a standard size cookie scoop, use 2 scoops per muffin.
  • Sprinkle 1 tsp of mini chocolate chips on top of each muffin.
  • Bake at 350 degrees F for 22-24 minutes.


YouTube video


Calories: 155kcal

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5 from 2 votes

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