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Healthy Pumpkin Chocolate Chip Muffins on a plate with the one on top split in half with butter in it.

Pumpkin Chocolate Chip Muffins

These healthier pumpkin muffins are moist, sweet, and delicious…and easily freezable. We pull them out of the freezer for snacks or for an easy breakfast.

Yield: 24 muffins 1x
Prep: 15 minutesCook: 18 minutesTotal: 33 minutes


  • 2 1/2 cups white whole wheat flour (sub: 1 1/2 cups whole wheat + 1 cup all purpose flour)
  • 1/2 cup ground flaxseed (sub: oats)
  • 1 cup sugar (use coconut sugar for a healthier alternative)
  • 2 teaspoons baking soda
  • 1 teaspoon baking powder (I like this aluminum-free kind.)
  • 2 teaspoons cinnamon
  • 1/2 teaspoon salt
  • 1 1/2 cups (or one 15 ounce can) pumpkin puree
  • 2/3 cup avocado oil or melted coconut oil
  • 1/2 cup unsweetened applesauce
  • 3 large eggs
  • 1 teaspoon pure vanilla extract
  • 1 cup semi sweet chocolate chips

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Make It Now:

  1. Preheat oven to 350°F. Grease two 12-cup muffin tins or line them with paper liners. 
  2. In a large mixing bowl, combine the flour, flax, sugar, baking soda, baking powder, cinnamon, and salt.
  3. In a smaller bowl, whisk together the pumpkin puree, oil, applesauce, eggs, and vanilla extract.
  4. Stir wet mixture into dry ingredients; mix just until combined (do not over mix). 
  5. Stir in the chocolate chips.
  6. Spoon the batter into the prepared muffin tins until each one is almost full. 
  7. Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean, about 20-22 minutes for two pans (or 18-20 for one). Note: Silicone pans will take a few minutes longer to bake. To check for doneness, insert a tooth pick and if it comes out clean then muffins are done. (Freezing instructions begin here.)
  8. Let cool on a cooling rack for 10 minutes in the tin. Remove muffins and place on the cooling rack a bit longer.

Freeze For Later: Bake muffins as directed in recipe. Let cool completely. Then place in a gallon-sized freezer bag or container, seal tightly, and store for up to 3 months. 

Prepare From Frozen: Thaw muffins in the refrigerator or warm in the microwave.


Dairy-Free Version: Omit the chocolate chips or use a dairy-free brand like Enjoy Life Chocolate Chips.

Gluten-Free Version: Use our gluten-free Pumpkin Muffin recipe instead. It’s very similar and uses coconut flour instead of wheat flour.

Pumpkin Alternative: You could use butternut squash puree instead of pumpkin. Here’s how to make butternut squash puree. Or try using sweet potato puree.

© Author: Rachel Tiemeyer
Cuisine: American Method: Bake