Healthy Pumpkin Applesauce Muffins

These pumpkin applesauce muffins with real chunks of apples and walnuts are so light and fluffy, your family will have no idea they’re actually good for you!

A hand grabbing a pumpkin applesauce muffin from a stack with a white background

Apples are a big deal here in Michigan. In fact, my house is within just a few miles of countless apple farms. Sweet, tart, sour, crisp, juicy – you name it, we eat it. These little gems started popping up at my farmer’s market in early August, and each week brings more varieties as the season progresses. I couldn’t help but mix the delicious apple with another fall favorite: pumpkin! I don’t do much baking, but these Healthy Pumpkin Applesauce Muffins are the perfect grab-n-go breakfast or afternoon snack- and are kid approved!


  • Whole wheat pastry flour: The whole grains add fiber and additional nutrients that you wouldn’t get from using white flour.
  • Flax seed: Finely ground, it doesn’t do much to the taste or texture, but adds omega 3 fatty acids and other nutrients.
  • Brown sugar: Sweetens the muffins.
  • Warm spices: Cinnamon, nutmeg, ginger, and cloves give these muffins a warm, almost pie like taste.
  • Baking soda and baking powder: Helps the muffins to rise.
  • Salt: Balances and enhances the other flavors.
  • Eggs: Acts as the binding agent to the muffins.
  • Pure pumpkin: Adds that delicious pumpkin flavor, as well as adds moisture, and vitamins to the muffins.
  • Yogurt: The acidity in yogurt reacts well with the baking soda to help with the leavening.
  • Applesauce: Adds moisture, sweetness, and also helps to bind the muffins.
  • Coconut oil: Adds moisture, and is a bit healthier option than using vegetable oil.
  • Apple: They bake in the muffins to be soft, sweet, almost caramelized clumps of goodness.
  • Walnuts: Adds protein, and a wonderful, crunchy, textural element to the muffins.
Ingredients for making pumpkin applesauce muffins

How to Make Healthy Pumpkin AppleSauce Muffins

Liz standing behind a counter with a bowl of dry ingredients for pumpkin muffins and a whisk resting inside

You’ll start your pumpkin applesauce muffins by taking all of your dry ingredients and whisking them together.

Liz's hand whisking wet ingredients inside a large glass measuring cup

Then in a separate bowl, you’ll whisk together all of your wet ingredients. Then slowly pour the wet into the dry and mix until combined.

Liz's hands cupped full of chunks of apples being poured into the batter for pumpkin applesauce muffins in a glass bowl

Then you’ll add the chopped apples and walnuts to your batter and mix again, gently.

Liz's hand holding a scoop full of pumpkin muffin batter being poured into a muffin tin

Next, in a prepared muffin tin (with or without liners is fine), evenly scoop your batter into each section. Then take your small mixture of remaining brown sugar and walnuts and sprinkle on top of each. Then toss in the oven at 375 for about 25 minutes, or until a toothpick comes out clean.

Healthy pumpkin applesauce muffins.

Once finished baking, let cool a couple minutes in the muffin tin before removing and then let them finish cooling on a cooling rack. Serve warm, topped with butter, and enjoy your Pumpkin Applesauce Muffins!

Frequently Asked Questions

What is the same as pumpkin puree?

Canned pumpkin and pumpkin puree are the same thing, not to be confused with pumpkin pie filling. You can also make your own pumpkin puree by baking your pumpkin and then scraping off the meat and pureeing it yourself!

What can I use instead of applesauce in baking?

You could use mashed banana, puree your own apples, or use more pumpkin puree.

How do I store baked muffins?

Keep in an airtight container. They’ll be good at room temperature for 3 days, or in the fridge for up to a week.

Pumpkin applesauce muffins.

More Pumpkin Goodies

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Liz standing in a kitchen using a knife to spread butter on a pumpkin applesauce muffin

These tender and moist pumpkin applesauce muffins are the perfect healthy breakfast to grab on your way out the door. They’re sweet and kid-approved, too, so you can feel good about your kids asking for seconds!

No fork required.

Healthy Pumpkin Apple Sauce Muffins 0015 WEB

Healthy Pumpkin Applesauce Muffins

4.57 stars average
These pumpkin-packed muffins with apples and walnuts are so light and fluffy your family will have no idea they’re actually good for you!
PREP: 20 minutes
COOK: 25 minutes
TOTAL: 45 minutes
Servings: 12



  • Pre-heat oven to 375 degrees and line a muffin pan with baking cups.
  • In a medium bowl, whisk together dry ingredients: flour through baking soda. *Use only 1/2 cup of the brown sugar.*
  • In a large bowl, whisk together wet ingredients: eggs through melted coconut oil.
  • Slowly add the dry ingredients to the wet and stir until fully incorporated.
  • Scraping down the sides of the bowl with a rubber spatula then stir in chopped apples and all but two tablespoons of chopped walnuts.
  • Using a large cookie scoop, divide the batter evenly between the 12 muffin cups.
  • In a small bowl, combine remaining 2 tablespoons walnuts and 2 tablespoons of brown sugar and carefully sprinkle the top of each muffin with the mixture before placing pan in the oven.
  • Bake for 25 minutes or until a toothpick comes out clean. Let cool 2 minutes in the pan then remove and continue cooling on a baking rack.


Calories: 152kcalCarbohydrates: 16.5gProtein: 5.3gFat: 8.1gSaturated Fat: 3.2gPolyunsaturated Fat: 4.9gCholesterol: 37mgSodium: 202mgFiber: 3.8gSugar: 3.1g

35 thoughts on “Healthy Pumpkin Applesauce Muffins”

  1. Do you add the pumpkin raw or do you cook or bake it in the oven until soft? Would like to try the recipe but got this doubt. Another question, as not living in the States we do not have apple sauce in Colombia, I substitute with normal sugar or honey?

    1. I made these muffins for my husband last week, he is diabetic and most muffins have too many carbs. He absolutely loved these and can fit them in his diet with inly 16.5 carbs each!I am sure he will be asking for more when they are gone!!! Thank you for this recipe, I am sure it will be a staple in our house from now on!

  2. I toasted up a big batch of nuts last week and have been eating my way through them as snacks all week long! I love the idea of stuffing them into muffins also. Especially pumpkin perfect muffins!

  3. Thanks for this wonderful recipe. I am joining the chorus as I add walnuts to everything. It just doesn’t taste right to me without that crunch. My husband is a diabetic. I pack him a lunch everyday of mini meals. A healthy muffin is always included. Can’t wait to make these for him. He’s going to love them…me too!

  4. I had such a lovely day in the orchards cracking nutty jokes with you! Your son just melts my heart – “mix muffins”! Was his first word was something food related too? These muffins do sound worthy of missing naps for! I can’t wait to see what other nutty recipes you come up with:)

  5. Yummy! These look fabulous! Love the combination of flavors! Did you pick those walnuts yourself? I have never seen a walnut in its shell before! Congrats on Diamond, that is very exciting! These would be a great runner snack!

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