These Healthy Pumpkin Chocolate Chip Muffins are loaded with warming fall spices and are healthier than your average muffin. These muffins can be made directly in a bowl and are perfect to enjoy for breakfast or a snack!

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.

These muffins have similar ingredients to my Healthy Pumpkin Bread and Healthy Chocolate Pumpkin Bread but are made with cane sugar or coconut sugar rather than maple syrup for a sweet and fluffy texture. These muffins are also loaded with dark chocolate chips to give them that chocolatey flavour in every bite.

Enjoy these Healthy Pumpkin Chocolate Chip Muffinfor 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

  • All the best Fall flavours. 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!
  • Versatile and customizable.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. You can also add in any mix-ins you love to this recipe.
  • Easy to make. 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

Step 1

Mix the flour, sugar, baking powder, baking soda, salt and pumpkin spice together in a large mixing bowl until no clumps remain. Make sure to measure out your flour accurately. (If you’re not sure how to do this, refer to this guide.)

a clear mixing bowl with flour in it

Step 2

Mix the pumpkin puree, apple cider, eggs, melted coconut oil and vanilla extract together in a separate bowl. Make sure that the coconut oil is cooled and at room temperature. If you add the coconut oil to the eggs while it’s still hot it will end up cooking the eggs.

pumpkin puree in a clear mixing bowl

Step 3

Pour the bowl with the wet ingredients into the bowl with the dry ingredients and gently mix together to combine using a folding motion with the spatula. Don’t overmix the batter otherwise you’ll end up with dense muffins.

pumpkin muffins batter in a clear mixing bowl

Step 4

Once the batter is mixed, add in the dark chocolate chips and gently give it another mix to incorporate the chocolate chips into the batter.

pumpkin muffin batter and chocolate chips in a clear mixing bowl

Step 5

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. Sprinkle more chocolate chips on top.

unbaked pumpkin chocolate chip muffins in a muffin pan

Step 6

Bake at 350 degrees F for 20-22 minutes or until a toothpick comes out clean.

baked pumpkin chocolate chip muffins in a baking 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!

How to store these muffins

Store any leftover muffins in a sealed container on the counter for up to 5 days or in the fridge for up to 7 days. If storing in the fridge, you may want to slightly warm the muffins in the microwave before eating.

This recipe is also freezer-friendly. To freeze the muffins let them cool completely on the countertop then transfer to a freezer bag and place in the freezer for up to 2 months. Defrost on the counter and warm in the oven.

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

If you tried these Healthy 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!

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three pumpkin chocolate chip muffins stacked on top of each other

Healthy Pumpkin Chocolate Chip Muffins

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


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


Units Scale
  • 1 3/4 cup spelt flour (can sub 1-1 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 and cooled
  • 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: healthy pumpkin muffins, pumpkin muffins with chocolate chips, chocolate chip pumpkin muffins healthy