Healthy Chocolate Chip Pumpkin Muffins

by Heidi @ Food Doodles on October 23, 2015

These healthy chocolate chip pumpkin muffins are soft, fluffy and 100% whole wheat but you’d never guess it!

I am so ready for pumpkin!  Who’s with me?

I know some people were waiting for September before they started posting pumpkin recipes but I had to wait until it felt right.  Our summer seemed to go on for a long time this year, I just couldn’t post pumpkin things any earlier!

Now I am ready though.  Things are finally cooling off, it feels like fall!  These healthy chocolate chip pumpkin muffins are the perfect way to start pumpkin season 🙂

Pepita Chocolate Chip Pumpkin Muffins Image

I need to tell you that my kids love these muffins.  My son has been eating these like crazy.

I made a big batch of 24 and they’re almost already gone even though I just made them!  They’re so good.

I don’t like my muffins too sweet, so I put a small note in the recipe, if you prefer your muffins sweeter you can always add a little more sugar 🙂  My kids like these just the way they are and I agree with them.

Let’s just say my kids have not been the only reason these are going fast 🙂

I added some pepitas for a nutritional boost and used less sugar than you find in most pumpkin muffin recipes. I used white whole wheat flour but regular whole wheat or even all-purpose flour would also work.

Pepita Chocolate Chip Pumpkin Muffins Image

I hope you’ll give these healthy pumpkin muffins a try!

Healthy Chocolate Chip Pumpkin Muffins
Prep Time
20 mins
Cook Time
20 mins
Total Time
40 mins
Course: Breakfast, Snack
Servings: 12 muffins
  • cups white whole wheat flour
  • 1 teaspoon baking powder
  • ¼ teaspoon baking soda
  • 2 teaspoons cinnamon
  • ¾ teaspoon ginger
  • ¾ teaspoon cloves
  • ¾ teaspoon nutmeg
  • ½ teaspoon fine sea salt
  • ½ cup salted butter or coconut oil softened
  • ¾ cup brown sugar
  • 2 large eggs
  • 1 teaspoon vanilla
  • ¾ cup pumpkin puree
  • ¾ cup semi sweet chocolate chips
  • 3/4 cup pepitas
  1. Preheat oven to 350°F. Prepare a muffin tin with paper liners or by lightly greasing or buttering. Set aside.
  2. In a medium sized bowl combine the flour, baking powder, baking soda, spices and salt. Stir to combine and set aside.
  3. In a bowl with a handheld mixer or the bowl of your stand mixer beat the butter until soft and fluffy. Beat in the brown sugar until combined.
  4. Add the eggs one at a time beating until combined. Add the vanilla and beat into the mixture.
  5. Add the pumpkin and beat until combined again before adding the dry ingredients.
  6. Mix until mostly combined before adding the chocolate chips and pepitas. Finish mixing just until everything is combined.
  7. Divide batter evenly among the 12 cavities in the muffin tin. Sprinkle tops with extra chocolate chips and Pepita if desired. Place in the oven and bake 17-20 minutes until a toothpick inserted in the center comes out clean.
  8. Remove muffins from the muffin tin and place on a cooling rack until cool. Once completely cool, muffins can be stored in an airtight bag or container for up to 5 days or frozen for up to 3 months.
Recipe Notes

I prefer my baked goods to be barely sweet so if you prefer yours sweeter, consider adding 1/4 C extra sugar 🙂

To make these dairy-free, use coconut oil and make sure your chips are dairy-free.

Pepita Chocolate Chip Pumpkin Muffins Image

100% Whole Wheat Pepita Chocolate Chip Pumpkin Muffins

Leave a Comment

{ 4 comments… read them below or add one }

1 Charlotte Moore October 23, 2015 at 05:50

These look very good. Our oldest grandson (24) loves pumpkin bread. I know he would go for these. I fixed him and his other grandpa pumpkin pancakes last Saturday. They hunt in our woods so I fixed them pancakes one Saturday and now years later it is still a habit. Ha!!


2 Heidi @ Food Doodles October 23, 2015 at 09:50

I think that’s a great tradition. I know I would appreciate that 🙂 What do they hunt for?


3 Charlotte Moore October 23, 2015 at 09:58

They turkey hunt but deer hunt mostly. They have gotten several deer over the years. They eat lots of venison.


4 Heidi @ Food Doodles October 23, 2015 at 10:24

Nice! We mostly hunt for whitetail deer in our area, although some people hunt elk as well(my husband was thinking of trying to get a turkey, but I don’t know about that, hehe!). My husband gets a deer most years. I actually got my hunting license just this year but I haven’t gotten anything yet 🙂


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