Decadent Yet Healthy Chocolate Chip Pumpkin Muffins! Believe it or not, these pumpkin chocolate chip muffins are pretty healthy for you and are still the best tasting chocolate chip pumpkin muffins recipe! Read on to see how you can healthy these up a bit!

Chocolate Chip Pumpkin Muffins
Chocolate Chip Pumpkin Muffins

My Chocolate Chip Pumpkin Muffins are a family favourite.

This is the best recipe I have ever put together that uses whole wheat flour in a muffin, and you can’t even tell, which is the kicker for me. Why eat something that’s whole wheat just because it’s healthier, but you don’t really enjoy it that much. I also love that applesauce replaces the oil just as easy as pie, and I actually prefer them made with applesauce for that little extra flavor. This isn’t a recipe that compared to the store bought junky pumpkin muffins that are loaded with preservatives and oils. This recipe is for just darn good tasting, not too bad for you pumpkin muffins!

Can I freeze these muffins?

Yes! These pumpkin muffins are perfect for school lunches for the kids ( and hey some work lunches for Mom and Dad). Wrap them up tightly in a bag and make sure it’s sealed so that they don’t get freezer burned.

The Ultimate Chocolate Chip Pumpkin Muffins from @kitchenmagpie

How can I make these pumpkin muffins healthier?

  1. There is very little sugar to start with in these pumpkin muffins  and what I use is brown sugar instead of white.
  2. Use only 1/2 cup of chocolate chips instead of the usual entire cup of chocolate chips, it cuts the calories down.
  3. You also need large amounts of spices to make up for the lack of sugar in the base, and the amounts I add make up for it nicely.
  4. These chocolate chip pumpkin muffins out as beautifully rounded topped muffins even when you use the applesauce instead of the oil.
  5. The whole wheat flour is the key!

The Ultimate Chocolate Chip Pumpkin Muffins from @kitchenmagpie

Tips & Tricks For Baking  Chocolate Chip Pumpkin Muffins

  • Do not over mix the batter! Pumpkin will go rubbery on you if you do and then your muffins will bounce!
  • I find it’s better not to use liners when you don’t have oil in the recipe. When you use applesauce the muffins will stick to the muffin liners – a lot!
  • The chocolate chip pumpkin muffins shown in the photos have oil, that’s why I used a liner.

Healthy, Hearty and Has chocolate. The three H’s. Yum!

More  Recipes to Try!

  1.  Whole Wheat Hermit Cookies
  2. Chocolate Chip Banana Bread Scones
  3. Strawberry Plum Crumble Cake
  4. The Best Bakery Style Blueberry Muffins Ever

Happy Baking!




Don’t forget to PIN THIS RECIPE to your BAKING or PUMPKIN board and remember to FOLLOW ME ON PINTEREST!

The Ultimate Chocolate Chip Pumpkin Muffins. #pumpkin #chocolate #muffin


5 from 2 votes
The Ultimate Chocolate Chip Pumpkin Muffins
Prep Time
5 mins
Cook Time
15 mins
Total Time
20 mins
Whole wheat, applesauce and chocolate chips make these truly the ultimate Chocolate Chip Pumpkin Muffins!
Course: Breakfast
Cuisine: Muffins
Keyword: pumpkin muffins
Servings: 12 muffins
Calories: 158 kcal
Author: Karlynn Johnston
  • 2 eggs
  • 1 cup of pumpkin
  • 3/4 cup of brown sugar
  • 1/3 cup of oil or applesauce
  • 1/4 cup of water
  • 1 1/2 cups of whole wheat flour
  • 1/2 tsp baking soda
  • 2 tsp baking powder
  • 1/2 tsp cloves
  • 1/2 tsp nutmeg
  • 1 tsp cinnamon
  • 1/2 cup chocolate chips
  1. Preheat your oven to 375°F.
  2. Crack the eggs into your mixing bowl and mix.
  3. Add in your oil or applesauce, I only had oil in my cupboards this time, and I really wish I had the applesauce instead, it's so much healthier and adds a nice natural sweetness to the recipe.
  4. Add in the pumpkin and water. Stir.
  5.  Stir in the brown sugar until dissolved as much as possible.
  6. In another bowl, whisk together the flour, spices, baking soda and powder. Add in your chocolate chips.
  7. Mix them into the  wet mixture until just combined. When baking with pumpkin, you can't over handle it or the end baked result goes rubbery. Add the dry mix into the wet, and very gently mix it together until just...JUST....mixed.
  8. Fill the muffin tins to about 3/4 full. Bake them at 375 for 15 or so minutes until done.
Nutrition Facts
The Ultimate Chocolate Chip Pumpkin Muffins
Amount Per Serving (1 muffin)
Calories 158 Calories from Fat 18
% Daily Value*
Total Fat 2g 3%
Saturated Fat 1g 5%
Cholesterol 28mg 9%
Sodium 73mg 3%
Potassium 204mg 6%
Total Carbohydrates 31g 10%
Dietary Fiber 2g 8%
Sugars 19g
Protein 3g 6%
Vitamin A 17.6%
Vitamin C 1.1%
Calcium 7%
Iron 5.8%
* Percent Daily Values are based on a 2000 calorie diet.



Hey guys, I'm Karlynn! Welcome to The Kitchen Magpie, my website full of family friendly recipes, cocktails & homesteading tales of chickens & cows from the family farm! Make sure to check out my bestselling cookbook, Flapper Pie & a Blue Prairie Sky ,stay tuned for info on my second cookbook!


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    • thekitchenmagpie Reply

      @Milly Yes, they are exceptionally good freezer muffins!

  4. I’m just going through your blog now (Was looking at the blue berry scones). I really like how you have pictures for every step. It’s really helpful! Processing and freezing the pumpkins is a good idea. I need to do that myself this year. Do you just puree them in a blender and then freeze everything?

  5. My mom and I peeled my Halloween pumpkins, boiled the good inside part, and then mashed them, and put them in separate bags, each holding a cup so you didn’t have to measure. Best idea my mom ever had, and I had natural pumpkin for baking ALL this past year! It does take some effort but boy, its worth it and I can’t wait to get another years supply done. I also have a great blender this year to aid me instead of mashing.

    Thanks for the compliments, I love taking the pictures, it’s fun!

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