Nothing beats a delicious muffin! Light, fluffy, and moist, these Pumpkin Chocolate Chip Muffins check all the boxes. Made with 10 ingredients and they’re freezer-friendly too.
Pumpkin season is in full swing! Did you see my recent Pumpkin Chocolate Chip Bread recipe? Well, today I’m back with another pumpkin-flavored recipe, this time — muffins! These are such a great grab-and-go snack or breakfast (they go so well with my Breakfast Egg Muffins Recipe), when in a rush, we just grab one to enjoy on our walk to school.
If you’re looking for more muffin recipes to enjoy, try my Blender Banana Oatmeal Muffins, Almond Flour Cranberry Muffins, and Gluten-free Carrot Muffins.

Even better is that these pumpkin chocolate chip muffins are freezer-friendly, so you can make a large batch and enjoy whenever you choose to in the upcoming months.
It makes the holiday season so easy, as sometimes it’s so busy, we don’t get a chance to prep some wholesome treats for ourselves.
A Pumpkin Muffin Recipe for Everyone
While this muffin recipe is gluten-free. Information for that will be down below in the recipe variation section. It’s a recipe that everyone can enjoy!
These pumpkin chocolate chip muffins are also great for bake sales and school parties since they’re a nut-free recipe as well. They can be made ahead of time, so you don’t have to frantically bake these the night before. However, if your kiddo informs you of a bake sale the night before, not to worry, these pumpkin chocolate chip muffins only take 40 minutes from start to finish, so you can whip up a batch in a jiffy.
How to Make this Healthy Pumpkin Chocolate Muffin Recipe
Ingredients
- Eggs — room temperature is preferred
- Coconut sugar
- Pumpkin puree — you can use canned or homemade. Here’s how I make homemade pumpkin puree.
- Almond flour — double check that you’re using almond flour and not almond meal
- Coconut flour
- Baking soda
- Baking powder
- Pumpkin pie spice — it is a mix of cinnamon, ginger, nutmeg, allspice, and ground cloves.
- Salt
- Chocolate chips

Instructions
Prep the Oven and Pan
- Preheat oven to 350ºF and line a muffin tin with paper liners or use a silicone muffin tin. Set aside.
Mix the Wet Ingredients and Dry Ingredients Separately
- In a large bowl, mix together eggs, coconut sugar, and pumpkin puree.
- In a medium bowl, add almond flour, coconut flour, baking soda, baking powder, pumpkin pie spice, and salt.
- Mix everything together until all is combined, then gently fold in the chocolate chips.
Fill the Muffin Tin and Bake
- Divide the batter among the prepared muffin cups.
- Sprinkle with additional chocolate chips as desired. This gives it more of a “cafe-style” look with the chocolate chips on top!
- Bake for 20-25 minutes, until the tops of the muffins are set.
- Let cool before enjoying

Tips and Notes:
- Baking times may vary because ovens vary in power and efficiency. To check if your healthy pumpkin chocolate chip muffins have baked through, poke a toothpick into them. When removed, if the toothpick comes out clean, it’s done baking. If there is batter on it, continue to bake.
- Only fill each muffin cup three-quarters of the way up. It’s about two and a half tablespoons per muffin cup.
- If you’d like to make these pumpkin chocolate muffins ahead of time, you can make the batter in advance and place it in the fridge for up to one day beforehand.
- Be careful not to overmix the batter. Too much mixing will cause the pumpkin muffins to come out dense instead of light and fluffy.
Recipe Variations For These Pumpkin Muffins
- Chocolate chips can be swapped with any type of “chips” such as white chocolate chips, butterscotch chips, caramel chips, etc, in this healthy pumpkin chocolate chip muffin. You can even do a half-and-half mix of two flavors!
- Muffins can also be topped with other items such as coconut flakes, chopped nuts, seeds, dried fruit, etc.

Pumpkin Chocolate Chip Muffins
Ingredients
- 3 eggs large
- 3/4 cup coconut sugar*
- 1 cup pumpkin puree not pumpkin pie filling
- 3 cups almond flour
- 2 tablespoons coconut flour
- 1 tsp baking soda
- 1 tsp baking powder
- 1 tbsp pumpkin pie spice
- 1/4 tsp salt
- 1/4 cup chocolate chips save more for topping
Instructions
- Preheat oven to 350ºF. Line a muffin tin with paper liners or use silicone muffin tin. Set aside.
- In a large bowl, mix together eggs, coconut sugar, pumpkin puree and eggs.
- In a medium bowl add almond flour, coconut flour, baking soda, baking powder, pumpkin pie spice and salt. Mix everything together until all is combined.
- Fold in chocolate chips. Divide the batter among the prepared muffin cups. This is very important: fill each muffin cups three-quarters of the way. It’s about two and a half tablespoon per muffin cups. The dough will be a bit thick, but it will work perfectly. Sprinkle with additional chocolate chips as desired.
- Bake for 20-25 minutes, until the tops of the muffins are set and a toothpick inserted in the center comes out clean.
- Place the pan on a wire rack and let the muffins cool completely. It’s about 30 minutes. Enjoy!
Notes
- Avoid overfilling the muffin liner as it’ll overflow. Don’t add more than two and a half tablespoons per muffin cup.
- Avoid overmixing the batter or the muffins will become tough.
- To store: Store the muffins in the fridge for up to a week or on the counter for 3 days. Make sure they’re in an airtight container.
- To freeze: You can freeze the muffins for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Did You Make This?
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Can you use whole wheat flour instead of almond and coconut flours?
Sorry I’m not sure because I’ve never made this recipe with whole wheat flour!