Healthy pumpkin chocolate chip muffins made with whole wheat flour, coconut oil, and sweetened with honey. A perfect fall breakfast to enjoy during pumpkin season!
I don’t go overboard for every pumpkin-spiced product each autumn, but I do stock up on canned pumpkin when it’s on sale. Pumpkin is such a useful ingredient for creating moist, flavorful, and nutritious baked goods.
Have you tried my pumpkin baked oatmeal and pumpkin pie overnight oats recipes yet?
These pumpkin chocolate chip muffins are a family favorite. They stay perfectly moist and are warmly spiced with cinnamon, nutmeg, ginger, cloves, and allspice. The balance of pumpkin, honey, and coconut oil creates a tender crumb that’s delicious for breakfast or as a snack.
I often make a double batch to freeze — then I have quick breakfasts ready for busy mornings.
These muffins are best enjoyed with a cup of coffee and a cozy blanket on crisp mornings. Highly recommended!
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Why you’ll love these Healthy Pumpkin Chocolate Chip Muffins:
Super Moist
The combination of honey, pumpkin, and coconut oil yields muffins that are tender and moist rather than dry or crumbly.
Full of Flavor
Warm spices — cinnamon, ginger, cloves, allspice, and nutmeg — give these muffins cozy, seasonal flavor.
Healthier Choices
This recipe uses whole wheat flour, coconut oil, and honey as lighter substitutions while still delivering great taste. Pumpkin adds fiber, vitamins, and antioxidants, making these a nutritious choice for breakfast or snacks.
Freeze Well
These muffins freeze nicely for up to six months when stored in an airtight container. Thaw at room temperature for a quick treat.
What you need to make healthy pumpkin chocolate chip muffins
Ingredients
Pumpkin puree – Use canned pumpkin puree or homemade pumpkin puree. Do not use pumpkin pie filling.
Coconut oil – Use a coconut oil that liquefies when warmed and solidifies when cooled; it contributes healthy fats and moisture.
Vanilla extract – Pure vanilla extract adds depth of flavor.
Honey – Raw honey or any honey you prefer works well as a natural sweetener.
Egg – Helps bind ingredients and provides structure.
Salt – Enhances the other flavors and balances sweetness.
Cinnamon – Essential for warm spice flavor.
Pumpkin pie spice – A blend of ginger, cloves, nutmeg, and allspice. Use store-bought or homemade.
Baking soda – Gives lift so the muffins are light and tender.
All-purpose flour – Combined with whole wheat flour for balanced texture.
Whole wheat flour – Adds heartiness and extra fiber.
Chocolate chips – Dark, semi-sweet, or mini chips all work. Dark chocolate pairs nicely with pumpkin.
Pecans – Coarsely chopped pecans add a toasty crunch on top and in the muffins; walnuts may be substituted or omitted.
Supplies
Mixing bowls, whisk, and spoon – For combining wet and dry ingredients.
12-cup muffin tin – Standard muffin pan.
Paper liners (optional) – Nonstick liners or a light spray of cooking oil will prevent sticking.
Healthy Pumpkin Chocolate Chip Muffins Recipe
Prep – Preheat the oven to 350°F (175°C). Line a 12-cup muffin pan with liners or lightly grease the cups.
Mix the wet ingredients – In a large bowl, whisk melted coconut oil and honey until combined. Whisk in the egg, then add pumpkin puree and vanilla. Beat until smooth.
Mix the dry ingredients – In a separate bowl, combine whole wheat flour, all-purpose flour, salt, baking soda, cinnamon, and pumpkin pie spice.
Combine – Add the dry mixture to the wet ingredients and stir just until combined; avoid overmixing. Gently fold in the chocolate chips and 1/2 cup of the chopped pecans. Let the batter rest for about 10 minutes.
Fill the muffin cups – Spoon the batter into the prepared muffin tin, filling each cup to the top. Sprinkle the remaining 1/2 cup of chopped pecans over the tops.
Bake – Bake for 20–25 minutes, or until a toothpick inserted into the center comes out clean. Let the muffins cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
Let cool – Allow the muffins to cool for 10 minutes in the pan before moving them to a cooling rack.
Tips for success
Substitutions – Swap walnuts for pecans or omit nuts if desired.
Don’t overbake – Check at 20 minutes. Gently press the tops; if they rebound, they’re done. If they sink, bake a few more minutes.
Storage – Store at room temperature in an airtight container for up to a week, or freeze for up to three months.
More pumpkin recipes on the blog:
If you enjoyed this recipe, try these other fall favorites from the blog.
- Healthy Pumpkin Overnight Oats
- Pumpkin Pie Baked Oatmeal
- Pumpkin Spice Hot Chocolate
I hope you love this easy pumpkin muffin recipe! If you make them, please come back and leave a comment and rating to let me know how they turned out.
Pin these steps to try later. Tag @athomeontheprairie on Instagram to share what you’ve made!
Healthy Pumpkin Chocolate Chip Muffins
12 muffins
15 minutes
25 minutes
2 minutes
42 minutes
Healthy and delicious pumpkin chocolate chip muffins made with whole wheat flour and sweetened with honey. A perfect breakfast for crisp fall mornings!
Ingredients
- 1 can pumpkin puree
- 1/3 cup coconut oil, melted
- 3/4 cup honey
- 1 large egg, at room temperature
- 2 teaspoons vanilla
- 1 cup whole wheat flour
- 1/2 cup all purpose flour
- 1 teaspoon baking soda
- 1 teaspoon ground cinnamon
- 1 teaspoon pumpkin pie spice
- 1/2 teaspoon salt
- 1/2 cup chocolate chips
- 1 cup pecans, coarsely chopped
Instructions
- Preheat the oven to 350 degrees and line a muffin pan with 12 liners or spray the pan lightly with cooking spray.
- In a large mixing bowl, whisk the coconut oil and honey together until completely combined. Whisk the egg, then add the pumpkin and vanilla extract. Beat until smooth.
- In a separate bowl, mix the flours, salt, baking soda, pumpkin pie spice, and cinnamon.
- Add the dry ingredients to the pumpkin mixture, stirring just until combined. Don’t overmix.
- Gently fold in the chocolate chips and 1/2 cup of the chopped pecans. Let the batter sit for 10 minutes.
- Spoon the batter evenly into the muffin tin, filling each cup to the top. Sprinkle the remaining chopped pecans on top.
- Bake for 20–25 minutes or until a toothpick inserted into the center comes out clean. Allow the muffins to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.
Notes
Substitutions – Walnuts can replace pecans or nuts can be omitted.
Don’t Overbake – Check after 20 minutes and press the tops lightly; if they bounce back they are done.
To Store – Keep in an airtight container for up to a week or freeze for up to three months.
Nutrition Information:
Yield: 12
Serving Size: 1 muffin
Amount Per Serving:
Calories: 287Total Fat: 15gSaturated Fat: 7gTrans Fat: 0gUnsaturated Fat: 7gCholesterol: 16mgSodium: 203mgCarbohydrates: 38gFiber: 4gSugar: 23gProtein: 4g