pumpkin chocolate chip muffins

Healthy Pumpkin Chocolate Chip Muffins Recipe

I love to whip up these Pumpkin Chocolate Chip Muffins in the oven in the morning and let them bake while we are getting ready for the day.  There is just something about fresh, warm baked spicy pumpkin-y smells in the house before breakfast that helps you get motivated and out the door for work or school.

These pumpkin chocolate chip muffins smell delicious, taste delicious, and disappear very quickly!  The spices in them make the house smell like Thanksgiving or Christmas on any ordinary day you make them.

pumpkin chocolate chip muffins on a plate

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Pumpkin Chocolate Chip Muffins

If you like to plan ahead, these healthy pumpkin chocolate chip muffins also freeze really well – although, we never have enough to freeze.  I usually make a double batch and they are all gone within a couple of days.

Healthy Pumpkin chocolate chip muffins

Originally, this recipe came from Allrecipes.com but it contained a lot of oil, much more sugar, and eggs so  I modified the basic idea with healthy alternatives such as applesauce and flax meal.  I use homemade applesauce, so I know exactly what goes into these muffins!

My favorite tools for making healthy pumpkin chocolate chip muffins are silicone muffin cups which make the whole cleanup process so much easier!  I used to wash my muffin pans every time I made muffins which diminished the frequency of muffins since I don’t enjoy washing muffin pans.  But since I’ve found these cute and colorful muffin cups, the clean-up is super easy!

The ease of making and eating muffins makes this recipe a keeper.  I have made a lot of different types of muffins but these healthy pumpkin chocolate chip muffins are my favorite recipe.  I always keep a can of pumpkin puree and some chocolate chips in my pantry so that I can make these delicious muffins often.

Create Your Own Healthy Pumpkin Chocolate Chip Muffin Mix

They would also be really simple to make ahead as a mix with all the dry ingredients in a zippered bag.  Label the bags so they are ready to add the applesauce, water, and pumpkin.  These muffins also travel really well in lunches (or breakfasts in the car) because they are moist but not crumbly.

Maybe our family is the only one around who sometimes eats breakfast on the way to school or work, but it’s really handy to have something that doesn’t leave a mess all over the seats or your lap!

If you love muffins and love an easy recipe that is full of flavor, then this is a recipe you will want to make and save for frequent use.  Filled with healthy goodness, these Pumpkin Chocolate Chip muffins will be your new favorite recipe!

5 from 6 votes

Pumpkin Chocolate Chip Muffins

Course Bread
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 12 Muffins
Author Karen Carlton


  • ½ C. sugar
  • ¼ C. applesauce
  • 2 T. Flax meal mixed with 6 T. water
  • ¾ C canned pumpkin
  • ¼ c. water
  • 1 ½ c flour
  • ¾ tsp. baking powder
  • ½ tsp. baking soda
  • ¼ tsp ground cloves
  • ½ tsp. ground cinnamon
  • ¼ tsp. salt
  • ¼ tsp. ground nutmeg
  • ½ c. Hersheys dark chocolate chips


  1. Mix all the ingredients together until completely mixed. Fill greased muffin pan 2/3 full of muffin batter. Bake at 400 degrees for 20-25 minutes.


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36 thoughts on “Healthy Pumpkin Chocolate Chip Muffins Recipe”

  1. Thanksgiving treats, here we come! Looks like a great snack or after dinner dessert option. Thanks for sharing. I bet if you don’t tell people they are Gluten Free, they could never guess. That is something I like to do from time to time with friends and family. You know the ones that think that everything gluten free tastes poor. We shall see… Thanks!

  2. These vegan pumpkin spice muffins look delicious! Also, I purchases silicone muffin tin liners (like the ones you recommended) about a year ago and they have been AMAZING!

  3. 5 stars
    I loooove making muffins but have actually never made pumpkin muffins even though I’ve meant to on several occasions. I’m adding these to my ‘to bake’ list. They look really good!

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