These Pumpkin Chocolate Chip Muffins are loaded with warming fall spices and healthy ingredients! The pumpkin puree and chocolate chips make these a deliciously light and fluffy muffin!

three pumpkin chocolate chip muffins stacked on top of each other

A healthy pumpkin muffin recipe

I love when I can put a healthier spin on a baked good recipe but still have it taste delicious. This recipe for pumpkin chocolate chip muffins is made healthier than the average recipe, by using ingredients like spelt flour, organic cane sugar, and coconut oil.

They also have less oil overall than a typical muffin without sacrificing that rich indulgent taste. These Healthy Gingerbread Muffins and Banana Nut Muffins are the perfect example – less oil, healthy ingredients, but incredibly tasty!

These muffins are perfect for a breakfast on the go, an afternoon snack with a cup of tea, or a little dessert in the evening.

Why you’ll love this recipe

  • These muffins combine flavours like vanilla, pumpkin spice, apple cider, pumpkin puree and chocolate – which results in a really decadent muffin that tastes like it was meant for fall!
  • These muffins are versatile and can be made with Spelt flour, (as the recipe calls for) regular flour or a 1-1 gluten-free flour blend.
  • This recipe is easy to make and can be whipped up using just 2 bowls and a spatula! No mixers or fancy equipment needed.

How to make pumpkin chocolate chip muffins

Mix the dry ingredients together in a large bowl and the wet ingredients together in a separate bowl.

Gently mix the dry and wet ingredients together just until combined. Don’t overmix! Then, add the chocolate chips and gently fold in.

Line a muffin pan with liners and spray with cooking spray to prevent sticking. Spoon the muffin batter into the moulds filling 3/4 of the way full. Bake for 20-22 minutes or until a toothpick comes out clean.

unbaked pumpkin chocolate chip muffins in a muffin pan

How to make homemade pumpkin pie spice

You can buy store-bought pumpkin pie spice which is easier to make this recipe, or even just use a combination of cinnamon and nutmeg to make a delicious muffin.

But if you’d like to make your own pumpkin pie spice, combine 2 tbsp ground cinnamon, 1 tsp ground ginger, 2 tsp ground nutmeg, 1/2 tsp ground allspice and 1/2 tsp ground cloves together. It’s a great spice blend to have on hand for the fall season!

baked pumpkin chocolate chip muffins in a baking pan

Tips for making this recipe perfectly

  • Make sure to use pumpkin puree and not pumpkin pie filling. The two are not the same! Pumpkin pie filling is sweetened and has a bunch of ingredients added to it. Pumpkin puree should only have one ingredient (pumpkin) on the label.
  • Don’t overmix the batter. This will result in a tougher and less fluffy muffin. It’s ok if there are a few small lumps in the batter.
  • Use a spatula to gently fold the batter together to prevent overmixing.
  • Only fill the muffin tin 3/4 of the way full, otherwise the muffin batter can overflow.
pumpkin chocolate chip muffins on a cooling rack

More pumpkin recipes to try

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three pumpkin chocolate chip muffins stacked on top of each other

Pumpkin Chocolate Chip Muffins

  • Author: Jess
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert, Breakfast
  • Method: Bake
  • Cuisine: American


The perfect fall muffin loaded with pumpkin, pumpkin spice and chocolate chips!


  • 1 3/4 cup spelt flour (can sub 11 gluten-free flour blend, or regular flour) 
  • 1/2 cup organic cane sugar or coconut sugar
  • 3/4 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 2 tsp pumpkin spice
  • 1 cup pumpkin puree
  • 1/4 cup+ 2 tbsp apple cider (can sub orange juice or milk of choice)
  • 2 eggs
  • 1/3 cup coconut oil, melted
  • 1 tsp vanilla extract
  • 1/2 cup chocolate chips


  1. Preheat the oven to 350 degrees F, line a muffin pan with muffin liners and spray them with cooking spray to prevent any sticking. 
  2. Mix all the dry ingredients together in a large mixing bowl, and the wet ingredients together in a separate mixing bowl.
  3. Pour the wet ingredients into the dry and gently fold together until combined. Don’t overmix. 
  4. Add the chocolate chips and mix together just until combined. 
  5. Spoon the batter in the muffin pan filling each mould 3/4 of the way full. 
  6. Bake for 20-22 minutes or until a toothpick comes out clean. 
  7. Let cool for at least 15 minutes before eating.


Make sure to use pumpkin puree and not pumpkin pie filling! The only ingredient on the can should be pumpkin. 

Don’t overmix the batter. This is result in a dense and less fluffy muffin. Use a spatula to just gently fold the ingredients together. 

Don’t fill the muffin moulds all the way to the top. This can cause the batter to overflow. 


  • Serving Size: 1 muffin
  • Calories: 190
  • Sugar: 12g
  • Sodium: 160mg
  • Fat: 8g
  • Saturated Fat: 6g
  • Carbohydrates: 28g
  • Fiber: 2g
  • Protein: 4g

Keywords: pumpkin muffins with chocolate, chocolate chip muffins with pumpkin

If you tried these Pumpkin Chocolate Chip Muffins or any other recipe on the blog let me know how you liked it by leaving a comment/rating below! Be sure to follow along on PinterestInstagram and Facebook for even more deliciousness!