Whole Wheat Pumpkin Muffins with Chocolate Chips

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Whole Wheat Pumpkin Muffins are always a hit, especially when dotted with mini chocolate chips. They taste indulgent even though they’re packed with plenty of healthy ingredients.

Whole Wheat Pumpkin Muffin Recipe with Chocolate Chips

I’m bidding farewell to zucchini and welcoming the season of all things pumpkin to The Dinner-Mom site! Wohoo!

I can’t think of a better way to kick things off than with these Whole Wheat Pumpkin Muffins. (Unless you are craving chocolate, in which case you will want to hop on over to Healthy Chocolate Pumpkin Muffins.)

Either way, they always seem to be exactly what I need. A quick breakfast? Pumpkin muffins to the rescue. After school snack? Lunch box treat? They’re always welcomed. A side for dinner? Edible gifts?

I’ve yet to find an occasion when these don’t deliciously do the trick. By the way, if you need a gluten-free version, check out Healthy Oatmeal Pumpkin Muffins. It’s based on this recipe, but replaces all of the flour with oats.

So what’s so special about these Whole Wheat Pumpkin Muffins?

Well…I’ve become a bit of a Muffin Maker this year. Zucchini muffins gave way to banana muffins and applesauce muffins. It was only a matter of time before pumpkin got its turn. In every case, I was able to make muffins that were “healthified” without sacrificing taste. This one is no exception. 🙂

Whole wheat pumpkin muffin recipe

They call for 100% whole wheat flour, yogurt instead of oil and just a little less sugar. I hope you can tell just how super moist they are!

Not that they needed it, but I added some mini chocolate chips for my chocoholic family. Raisins are also delish. Really…nothing needs to be added at all though.

And, if you don’t mix anything else in we’re talking about approximately 100 calories per muffin and only a bit more if you add in chips or raisins.

Whole Wheat Pumpkin Muffins with Chocolate Chips

So pumpkin muffin mayhem begins. I make up batches of the dry mix so it’s a matter of minutes to have these baking in the oven. I can’t think of a better way to welcome fall!

Whole Wheat Pumpkin Muffins with Chocolate Chips
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4.34 from 3 votes

Whole Wheat Pumpkin Muffins with Chocolate Chips

Whole Wheat Pumpkin Muffins are dotted with chocolate chips. They taste indulgent but are full of healthy goodness.
Prep Time10 mins
Cook Time25 mins
Total Time35 mins
Course: Snack
Cuisine: American
Servings: 12 muffins
Calories: 145kcal


  • 1 1/2 cup whole wheat pastry flour
  • 1/2 cup Stevia sugar blend or 2/3 cup sugar
  • 1/2 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1/2 teaspoon ground cinnamon
  • 15 ounce pumpkin puree
  • 1 egg beaten
  • 5.3 ounce non-fat Greek yogurt
  • 1/2 cup Mini chocolate chips or raisins


  • Preheat oven to 350 degrees F.
  • Combine flour, sugar, baking powder, baking soda, salt and cinnamon in a bowl.
  • Stir pumpkin, egg and yogurt into the dry mix.
  • Fold in mini chocolate chips.
  • Fill muffins tins lined with paper liners or coated with cooking spray about 2/3 full. (Tip: if using liners, give them a light spritz of cooking spray before filling with batter.)
  • Bake for 20-25 minute or until the muffins are firm and lightly browned on the top.
  • Allow muffins to cool for 5 minutes and then remove to a wire rack to cool further.


Calories: 145kcal | Carbohydrates: 27g | Protein: 4g | Fat: 2g | Saturated Fat: 1g | Cholesterol: 15mg | Sodium: 159mg | Potassium: 166mg | Fiber: 2g | Sugar: 14g | Vitamin A: 5550IU | Vitamin C: 1.5mg | Calcium: 46mg | Iron: 1.2mg
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More pumpkin muffin variations you might enjoy:





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  1. YAY for breaking out the pumpkin..I just did too!
    And these muffins? How much do you charge for shipping? 😉 Pinned!

  2. These muffins look amazing! Love that they are so healthy with the whole wheat 🙂

  3. Okay, these muffins look PERFECT.

  4. I love that these are a bit “healthified”. Muffins can be deceiving in the healthy department sometimes. Great recipe and not as much guilt.

  5. Love pumpkin and muffins! Let the pumpkin season begin!!

  6. Looks delicious!

  7. Pumpkin and Chocolate were made for each other.

  8. I am loving these muffins! I too am about to plunge into all things pumpkin! And I am loving how much healthier these muffins are than traditional ones!

  9. These look beautiful!!! I could eat a dozen of these right about now 🙂

  10. I can’t get enough pumpkin lately! These muffins look amazing, and I love how healthy they are! What a perfect fall breakfast!

  11. Without pumpkin, I would NOT exist! LOL!

  12. There’s few things I love more during the fall than pumpkin-anything with chocolate! These muffins look amazing, and I love that they’re whole wheat too.

  13. Pass these my way! They look wonderful!

  14. The Ninja Baker says

    Only 100 calories, Marjory? Oh, my goodness they look soooo deliciously decadent…But how can I not make them keeping in my mind all the good for you ingredients =)

  15. Looks great! Yum! Love that you’ve made them healthier- I always laugh when I see muffin recipes that are similar in ingredients to cupcakes!

  16. Yum! I’m through two cans of pumpkin already and it’s not even officially fall yet! It’s going to be a pumpkin packed season for sure 🙂

  17. Love this healthy pumpkin muffin – always looking for ways to reduce fat so I love the Greek yogurt!

  18. How do you get pumpkin puree? May be a dumb question- but is it store bought in a can or do you roast a pumpkin in the oven or….?

  19. Bring on the pumkin!!! These muffins look super duper moist and delicious. And it’s a healthyfied muffin? Count me in!

  20. These look amazing, they’ll be making an appearance in lunch boxes next week!

  21. I love pumpkin muffins!

  22. Pumpkin muffins are one of my favorites! I love that you made them whole wheat, too. Perfect for breakfast!

  23. Have you tried substituting agave nectar for sugar in this recipe? Just wondering if it works?!
    Looks delicious- going to try these tonight! Maybe with a pumpkin beer 😉

  24. I made these today. They are really good. I used Truvia baking blend instead of sugar and I added some pumpkin pie spice. My husband said I could make them again!

  25. Hello! Do you have the nutrition facts for these? I need to know the carb count for the diabetics in my family
    I made them and my family loved them! Great texture and taste

    • Thanks for your comment. Unfortunately, we do not have nutrition software at this time. 🙁 I sometimes use an app like My Fitness Pal to get some estimates though, like the calorie count that I provided.

  26. Hi these muffins came it delish! Only problem is they didn’t really rise up. Any reason why? Thanks!

    • Thanks for your comment. I’m really not sure why they didn’t rise because I make these at least once a week with no troubles. I had this happen on another recipe I make frequently (vegan chocolate cake) and I think my baking powder was stale…just a thought!

  27. Just made these. Hot out of the oven and delish. Good thing I doubled the recipe as my 10 year old son loves them. Calculated 3 weight watchers points per muffin. Yum.

  28. I’ve made these twice now and learned my lesson–double the recipe. They go fast. My family loves them! Today I used stevia sweetened chocolate and topped each muffin with a pecan. Great recipe; thank you!

  29. I loved finding a recipe that uses whole wheat and real pumpkin in place of oils. However, I would advise doubling the spices, it lacked a pop of flavor I love with Fall pumpkin dishes.

  30. Do you use plain or vanilla Greek yogurt?

  31. I know it’s not fall and pumpkin season, but I’ve had a can of pumpkin staring at me each time I open my pantry, so I just really wanted to make these. ???? I’m not a huge baker, so I can’t figure out what I did wrong. My muffins rose in the oven and then fell immediately and were very dense and heavy and kinda mushy in the middle. They were not pretty and fluffy like yours. Any ideas as to what I may have done wrong?

  32. These are awesome! I added some pumpkin pie spice and used kefir and a little oil since I didn’t have Greek yogurt and they turned out fantastic! Thanks!!

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