One of the oldest recipes on the blog, these failproof muffins are the only recipe you’ll need for pumpkin season! Soft, lightly spiced, and loaded with sweet chocolate chips in every bite, you’ll find yourself making them again and again.

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken this recipe
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The Best Healthy Pumpkin Chocolate Chip Muffins

Not only are they naturally sweetened with honey and bananas and made with wheat flour, but they also combine in a single bowl. That’s right! No mixer is required, meaning prep time is minimal, and cleanup is a breeze.

Great to make in bulk and take on the go, they’re perfect for weekday breakfasts or afternoon snacks. The only problem is in my house they never last long!

With a five-star rating and countless reviews, readers love them just as much as my family, saying:

“I love these so much. They’re amazing! I gave some to a friend who doesn’t usually like pumpkin treats and she loved them.” – Rose

“WOW this recipe is good. Delicious, light, moist. I made it without choco chips and my toddler and I are LOVING it. Just ate two right out of the oven—sorry not sorry.” – Erica

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

Pumpkin Chocolate Chip Muffins Healthy Ingredients

A big part of what makes these healthy pumpkin chocolate chip muffins so amazing is simply a combination of ingredients.

Even though you can make substitutions to some of the ingredients, which I do cover below. But for best results, follow the recipe as written:

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken
  • Coconut Oil: Refined coconut oil is neutral and ideal to use in this recipe. It has no distinct coconut taste or aroma like virgin or unrefined coconut oil.
  • Honey: Honey provides sweetness to the muffins. Maple syrup can be used as a substitute.
  • Eggs: You’ll need two large eggs for this recipe.
  • Bananas: Bananas make the muffins sweet and extra moist. Make sure to use ripe bananas and measure out the banana mash before adding it to the batter.
  • Pumpkin Puree: Canned pumpkin is the same as pumpkin puree. It simply means 100% pureed pumpkin. I had a reader ask if pumpkin pie filling and/or mix can be used instead. Normally pumpkin pie filling has added sweetener and other ingredients, therefore, I do not recommend it.
  • Milk: I used dairy milk for this recipe but non-dairy milk, such as almond milk will work as well.
  • Pumpkin Pie Spice: Also known as pumpkin spice, is a spice mix of cinnamon, ginger, nutmeg, cloves, and allspice.
  • Baking Soda: It helps the batter rise and make the muffins light. I do not recommend a substitute.
  • Vanilla Extract: Vanilla enhances the flavor of the muffins and makes them taste yummy.
  • Salt: I like to use kosher salt but a sea salt is a great option too.
  • White Whole Wheat Flour: Is a great middle between all-purpose flour and whole wheat flour. It’s mild in flavor and pale in color than whole wheat flour as it’s made with a different variety of wheat. But the nutritional value is similar.
  • Chocolate Chips: Semi-sweet or dark chocolate chips work. Keep in mind if using semi-sweet chips, the muffins will be sweeter.

How to Make Pumpkin Banana Pumpkin Chocolate Chip Muffins

Grab a large mixing bowl, a whisk, and a wooden spoon, and let’s make the batter:

  1. Whisk together the coconut oil and honey. Then add in the eggs.
  2. With a wooden spoon, stir in the bananas, pumpkin puree, milk, pumpkin pie spice, baking soda, vanilla extract, and salt.
  3. Gently stir in the flour just until combined. Do not overmix. And lastly, fold in the chocolate chips.
Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

4. Grease a 12-cup muffin pan and divide the batter evenly between the cups, filling all the way to the top.

5. Bake for 5 minutes at 425 F, then keeping the muffins in the oven, reduce the oven temperature to 350 F, and bake for additional 17-20 or until toothpick inserted in the middle comes out clean. Remove and cool on a cooling rack.

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

Gluten-Free Banana Pumpkin Chocolate Chip Muffins

Yes! Simply use a gluten-free all-purpose flour blend. Some of the readers had luck with Bob’s Red Mill 1-to-1 Baking Flour, as well as almond flour.

I personally made these pumpkin muffins with oat flour and they were as equally delicious.

How to Store Banana Pumpkin Chocolate Chip Muffins

Pumpkin chocolate chip muffins will keep at room temperature for up to 3 days. Thereafter, keep them stored in the refrigerator in a sealed container.

These muffins also keep well in the freezer in a freezer-safe bag or container for up to 3 months. Simply defrost individual muffins overnight in the refrigerator and then for a warm, just baked taste, pop them into a microwave for a few seconds or until gently warmed through.

Healthy Pumpkin Chocolate Chip Muffins FAQs

Why are my pumpkin muffins so dense?

The most common reason for muffins to turn out dense is overmixing the batter. Be careful to combine the ingredients just until no streaks remain.

Why didn’t my pumpkin muffins rise?

If your muffins don’t rise as they bake, it’s likely either because the batter was overmixed or the oven wasn’t hot enough. Make sure to allow plenty of time for it to heat up!

Why do the chocolate chips sink in my muffins?

Chocolate chips can sink because they’re heavier or moister than the muffin batter. To prevent this, simply toss them in a light coating of flour before folding them into the batter.

Why are my pumpkin muffins sticky?

If your muffins are sticky, they’re most likely underbaked and need a little longer in the oven. You’ll know they’re done when they’re fluffy and lightly golden, and a toothpick inserted into the center comes out clean or with just a few moist crumbs.

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

Leftover Pumpkin Puree?

Here are more recipes to make with canned pumpkin puree:

Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

Video: How to Make Healthy Chocolate Chip Pumpkin Muffins

Watch step-by-step on how to make these easy healthy pumpkin muffins.  

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If you try our chocolate chip pumpkin muffins, please leave a star rating and a comment letting us know how you liked the recipe.

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Healthy Chocolate Chip Pumpkin Muffins - made with coconut oil, white whole wheat flour, and sweetened with honey. These are by far the BEST healthy pumpkin muffins | littlebroken.com @littlebroken

Healthy Chocolate Chip Pumpkin Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 40 reviews
  • Author: Katya
  • Prep Time: 12 mins
  • Cook Time: 25 mins
  • Total Time: 37 mins
  • Yield: 12
  • Category: Dessert
  • Method: Baking
  • Cuisine: American
Print Recipe

Description

Super moist and lightly sweetened with honey, these chocolate chip pumpkin muffins make the perfect fall breakfast or on-the-go snack! Made all in one bowl with coconut oil and white whole wheat flour.

Ingredients

Units Scale
  • ⅓ cup coconut oil, in liquid form
  • ½ cup honey or maple syrup
  • 2 large eggs
  • 1 cup mashed ripe banana, about 2-3 bananas
  • 1 cup pure pumpkin puree
  • ¼ cup milk
  • 2 tsp. pumpkin pie spice
  • 1 tsp. baking soda
  • 1 tsp. vanilla extract
  • ½ tsp. kosher salt
  • 1 ¾ cups white whole wheat flour, measured correctly
  • ½ cup chocolate chips, semi-sweet or dark chocolate

Instructions

  1. Preheat the oven to 425 degrees F.
  2. Grease 12 cup muffin pan with non-stick cooking spray or if using liners, line with liners.
  3. In a large mixing bowl, whisk coconut oil and honey. Whisk in eggs.
  4. With a wooden spoon, mix in the mashed banana, pumpkin puree, milk, pumpkin pie spice, baking soda, vanilla extract, and salt.
  5. Add the flour and mix just until combined. Fold in the chocolate chips.
  6. Spoon the batter evenly into the prepared pan. You should be able to fill all 12 muffin cups.
  7. Bake for 5 minutes at 425 F degrees, then keeping the muffins in the oven, reduce the oven temperature to 350 F degrees, and bake for additional 17-20 or until toothpick inserted in the middle comes out clean.
  8. Place the muffin pans on a cooling rack to cool. Store cooled muffins, covered, at room temperature for up to 3-4 days.

Notes

  • Ingredient Substitutions: See post for all substitutions, including gluten-free options.

Nutrition

  • Serving Size: 1 muffin
  • Calories: 259
  • Sugar: 21.6 g
  • Sodium: 218.2 mg
  • Fat: 9.8 g
  • Carbohydrates: 40.5 g
  • Protein: 4.4 g
  • Cholesterol: 31.1 mg