The Ultimate Pumpkin Chocolate Chip Muffins

Whole wheat, applesauce and chocolate chips make these truly the ultimate Chocolate Chip Pumpkin Muffins!

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Decadent yet healthy pumpkin chocolate chip muffins! Believe it or not, these  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!

a piece of pumpkin chocolate chip muffin in a white tea cloth
pumpkin chocolate chip muffins

My Pumpkin Chocolate Chip 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.

close up of Ultimate Chocolate Chip Pumpkin Muffin in a white cupcake liner

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!

top down shot of Pumpkin Muffins with lots of chocolate chips on top

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


The Ultimate Chocolate Chip Pumpkin Muffins

Whole wheat, applesauce and chocolate chips make these truly the ultimate Chocolate Chip Pumpkin Muffins!
5 from 6 votes
close up of Ultimate Chocolate Chip Pumpkin Muffin in a white cupcake liner
Prep Time
5 minutes
Cook Time
15 minutes
Total Time
20 minutes
12 muffins
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 teaspoon baking soda
  • 2 teaspoons baking powder
  • 1/2 teaspoon cloves
  • 1/2 teaspoon nutmeg
  • 1 teaspoon cinnamon
  • 1/2 Cup chocolate chips


  • Preheat your oven to 375°F.
  • Crack the eggs into your mixing bowl and mix.
  • 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.
  • Add in the pumpkin and water. Stir.
  •  Stir in the brown sugar until dissolved as much as possible.
  • In another bowl, whisk together the flour, spices, baking soda and powder. Add in your chocolate chips.
  • 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.
  • Fill the muffin tins to about 3/4 full. Bake them at 375 for 15 or so minutes until done.

Nutrition Information

Serving: 1muffin, Calories: 158kcal, Carbohydrates: 31g, Protein: 3g, Fat: 2g, Saturated Fat: 1g, Cholesterol: 28mg, Sodium: 73mg, Potassium: 204mg, Fiber: 2g, Sugar: 19g, Vitamin A: 880IU, Vitamin C: 0.9mg, Calcium: 70mg, Iron: 1mg

All calories and info are based on a third party calculator and are only an estimate. Actual nutritional info will vary with brands used, your measuring methods, portion sizes and more.

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Karlynn Johnston

I’m a busy mom of two, wife & cookbook author who loves creating fast, fresh meals for my little family on the Canadian prairies. Karlynn Facts: I'm allergic to broccoli. I've never met a cocktail that I didn't like. I would rather burn down my house than clean it. Most of all, I love helping YOU get dinner ready because there's nothing more important than connecting with our loved ones around the dinner table!

Learn more about me

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Reader Interactions

Comments & Recipe Tips Share a tip or comment!

  1. YOUR BFF says

    These are excellent! Looking forward to making them again this fall.5 stars

  2. Milly says

    Do these freeze well? I’m thinking school lunches…

    5 stars

    • thekitchenmagpie says

      @Milly Yes, they are exceptionally good freezer muffins!

  3. Qwerty says

    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 stars

  4. Karlynn says

    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!

  5. CuriousChef says

    The Ultimate Pumpkin Muffins Recipe – @karlynn – great step by step photos!
    This comment was originally posted on Twitter

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