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!

In this Post: Everything you need for Healthy Pumpkin Applesauce Muffins
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!
Ingredients
- 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.

How to Make Healthy Pumpkin AppleSauce Muffins

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

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.

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

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.

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.

More Pumpkin Goodies
- Healthy Pumpkin Bread
- Fluffy Pumpkin Pancakes
- Pumpkin Pie Protein Smoothie
- Pumpkin Banana Oatmeal
- Pumpkin Spice Latte
Did you try this recipe and like it? The next time you make it, snap a picture and share it to your socials! Tag @thelemonbowl and #thelemonbowl so we can admire and share your dish.

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 Applesauce Muffins
Ingredients
- 1 ½ cups whole wheat pastry flour
- ½ cup ground flax seed
- ½ cup brown sugar + 2 tablespoons
- 2 teaspoons cinnamon
- 1 ½ teaspoons baking powder
- 1 teaspoon ground nutmeg
- 1 teaspoon ground ginger
- ½ teaspoon ground cloves
- ½ teaspoon salt
- ¼ teaspoon baking soda
- 2 eggs
- 1 cup pure pumpkin
- ½ cup plain low fat yogurt
- ½ cup applesauce (unsweetened)
- 2 tablespoons coconut oil (melted)
- 1 cup chopped apple
- ½ cup Chopped Walnuts (divided)
Instructions
- 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.
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?
I used canned pumpkin which is cooked and pureed. Do you have access to that? Regular sugar would be fine!
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!
I’m so glad you enjoyed them!!! Woohoo!! Have you tried my almond flour muffins?? https://thelemonbowl.com/almond-flour-berry-muffins/
That trip looked like so much fun and these muffins are calling my name! I add nuts to everything too, except my chocolate chip cookies, that’s one place they don’t belong ;)
So funny – I just had that debate with family this weekend!! I love walnuts in everything, even chocolate chip cookies, but a few of my relatives agree with you – haha.
That trip looked like so much fun, and these muffins look fab!
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!
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!
I totally agree Carmen!
The flavors in these muffins are wonderful!!!
I love Diamond Nuts – the best! And these pumpkin muffins look awesome with their walnuts studded all over it.
Thank you so much Naomi!
Asher is such a cutie pie. Trip looked so interesting and fun! And the muffins of course look fab.
Aww thank you. RIP afternoon nap. Thank goodness for muffins. ;)
YUM!!! Love using whole wheat and have been using more spelt lately.
I’ve been wanting to use spelt flour more!
OMG these look totally amazing Liz! Also, fascinating pictures of the walnut trip, looks like you ladies had so much fun!
Aww thank you so much! I loved how they turned out.
Great post, what a cool trip! The muffins look yummy!
Those walnuts look incredible, and the muffins! I love a good pumpkin muffin.
Same here Shaina! Pumpkins just really lend themselves to baked goods.
What a cool experience! I used to hate eating baked goods from my grandma, because she always added nuts to everything, but as I got older, I liked nuts in my baked goods more and more!
That’s so funny!!! I love adding nuts to my stuff..always have.
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:)
It was so fun getting to know you!! I think his first word is Dada but I’m trying to block that from memory. ;) xoxo
Ahhhh I love me a healthy muffin! Especially when it’s stuffed to the brim with all those goodies!
These look so good Liz! Love the pumpkin apple combo. The best flavors of the season in one muffin :) Your son is SO CUTE!!
I love Diamond nuts and I put walnuts in everything including my vegetable dishes. The muffins sound like my kind of breakfast! Looks like you had a great trip to California!
These muffins look soo good, and I love that they are healthy! I’m new to The Lemon Bowl, and I’m loving your blog! :)
Welcome Karen!! So glad you’re here!! :)
YUM these sound incredible!!! Making them!!! :)
I hope you love them Haley!
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!
I didn’t pick these particular ones but I love that I know where they come from! Thanks so much!! :) IDEAL runner food!