Healthy Chocolate Chip Pumpkin Muffins

September 21, 2016 by Katya 117 Comments Updated September 08, 2021

Super moist and lightly sweetened with honey, these healthy 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.

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The Best Healthy Pumpkin Muffins

Soft and lightly spiced healthy pumpkin chocolate chip muffins are a favorite during this time of the year. They make the best take-and-go breakfast and can double as a snack or even dessert.

They are sweetened only with honey and bananas, and instead of white flour, made with white whole wheat flour. And did I mention you only need one bowl, a whisk, and a spoon to make them? That’s right! No mixer is required.

Make a double batch to enjoy now and freeze for later. These pumpkin muffins keep well in the freezer for up to 3 months.

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

It’s All About the Right 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:

Coconut Oil: Refined coconut oil is neutral and ideal to use in this recipe. It has no distinct coconut taste or aroma like the 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 to the batter.

Pumpkin Puree: Canned pumpkin is 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 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 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 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 more sweeter.

Can You Make These Muffins Gluten-Free?

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 Make Healthy Pumpkin Chocolate Chip Muffins

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

Whisk together the coconut oil and honey. Then add in the eggs.
With a wooden spoon, stir in the bananas, pumpkin puree, milk, pumpkin pie spice, baking soda, vanilla extract, and salt.
Gently stir in the flour just until combined. Do not overmix. And lastly, fold in the chocolate chips.

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

To Store 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.

Leftover Pumpkin Puree?

Here are more recipes to make with canned pumpkin puree:

Pumpkin Cream Cheese Muffins
Pumpkin Bread
Pumpkin Chili
Pumpkin Pecan Granola
Pumpkin Bars with Cream Cheese Frosting

Video: Watch How to Make It!

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