To add to the internet explosion of all things pumpkin spice related this time of year, today I’m sharing my whole wheat pumpkin spice muffins. I am always trying to make healthier versions of some of our favorite snacks, and this recipe was a big win with my entire family.
One of the things I love about the recipe is that you can make them a couple of different ways. The first time I baked them I used chopped walnuts (see, there I go trying to make everything healthier). The next time I made them my oldest daughter requested that I put chocolate chips in them. She wanted them to be a little bit sweeter…Using both the pumpkin puree and applesauce makes these muffins incredibly moist which I think is a plus as well!
Ingredient Notes
Just a couple notes about the ingredients I used. Use pumpkin puree, not pumpkin pie filling. The two are usually right next to each other on the grocery store shelves. Pumpkin puree is just pureed pumpkin flesh. Pumpkin pie filling typically contains added sugar and spices in addition to the puree.
Look for applesauce with no added sugar. I often use Trader Joe’s Organic Unsweetened Applesauce, but I know there are several other brands out there without extra sugar. Read the ingredient list on the package if you are unsure.
The pumpkin pie spice I buy at Trader Joe’s when it makes its way onto shelves in late summer/early fall. If you don’t have a Trader Joe’s near you, other spice brands have their own version, so check your local grocery store.
I usually buy the Enjoy Life dark chocolate chips. I buy them for the higher cacao content and minimal ingredient list, but these are also a great alternative if you have allergies in your household. These dark chocolate chips are dairy, nut, and soy free. The ingredient list for this particular kind is just unsweetened chocolate and cane sugar.
You can find them on Amazon, at Target, or at several other specialty grocery stores. Enjoy Life also makes a semi-sweet version, as well as a mini chocolate chip version.
Recipe
After you whisk the dry ingredients together, set the bowl aside and use a second bowl for the wet ingredients. I’ve found it easiest to mix the pumpkin puree, applesauce, and honey together first, then add the milk and vanilla.
Mix until combined, but don’t over mix. You may still have some smaller lumps, but that is okay.
Finally, gently fold in the chopped walnut pieces or chocolate chips.
Baking Tips
My first baking tip is to enlist a little helper!
I typically use muffin liners when I bake these, but you can certainly do without them. The muffins come out of the liners much better on the second day, or after they have been allowed to cool for quite a bit. Or you could be like my three year old and just bite off any part of the muffin that sticks to the liner!
Fill the muffin cups 2/3 full and bake at 325 degrees for 20-22 minutes. My oven has been doing wonky things lately, so I have been baking at lower temperatures which worked out beautifully here. Allow to cool completely before you bite into one of these delicious whole wheat pumpkin spice muffins!
These whole wheat pumpkin spice muffins are the perfect fall snack, or even as an accompaniment to your morning coffee! Enjoy!
For more healthy snack ideas, check out my 25 Healthy Back-To-School Snack ideas. This list is packed with easy and healthy snacks that you can feel good about sending your kiddos off to school with (or eating yourself!).

- 1 1/2 cups whole wheat pastry flour
- 1 tsp pumpkin pie spice
- 1/2 tsp salt
- 2 tsp baking powder
- 1/2 tsp baking soda
- 1 cup pumpkin puree
- 1/4 cup unsweetened applesauce
- 1/2 cup honey
- 1/2 cup milk
- 1 tsp vanilla
- 3/4 cup chopped walnut pieces or chocolate chips
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Preheat oven to 325 degrees. Line a muffin tin with muffin liners or spray with cooking spray. Set aside.
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Whisk together the whole wheat pastry flour, pumpkin pie spice, salt, baking powder, and baking soda.
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In a separate bowl combine the pumpkin, unsweetened applesauce, and honey. Whisk in the milk and vanilla and mix until smooth.
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Add the dry ingredients to the wet and stir until combined. There may be a few small lumps left in the batter, but do not overmix.
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Gently fold in the chopped walnut pieces or chocolate chips if using.
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Fill muffin cups 2/3 of the way full. Bake 20-22 minutes or until toothpick inserted in the center of a muffin comes out clean. Let cool completely.
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Makes 12-15 muffins.
I need to try these! I love pumpkin spice everything 🙂
Jenna this is your time of year! Do you shop at Trader Joe’s? Everything in there is pumpkin spice flavored right now!
Yummy! These look delicious & easy to make!
These muffins are super easy to make!
My kids are really into making bread right now so I’ll have to try these. Love that they’re so healthy!
I love it when my kids get involved in helping in the kitchen! My oldest (12) can now bake on her own, and even leaves the kitchen pretty darn clean when she is done!
ooh, these look so yummy! I love pumpkin (call me basic I don’t care). It is so good. I love how your recipe is really healthy with the applesauce substitution. I will have to try these.
Thank you! Hope you get a chance to try them. I am always trying to make recipes healthier!
We were just talking about how we wanted to cook with some pumpkin. I would like to make a batch of these for the kids to have for breakfast.
We love baking with pumpkin this time of year. These muffins would definitely be great for breakfast!
These look delicious. And healthy! Can’t wait to make them with my little helper too. Everything tastes better when we make it together 🙂
I love cooking with my three kiddos. Hope your little helper enjoyed the muffins!
I love the combination of chocolate and pumpkin. These sound great!
Pumpkin and chocolate are one of my favorite combinations!
Love pumpkin. Great recipe for this season. I’ve never made muffing. Would be a great start for me.
These muffins are super easy Tayrina! Good luck and let me know if you have any questions!
My daughter and husband will love this. We love pumpkin, it’s been awhile since I made something with pumpkin. Thank you for sharing this recipe.
You are very welcome Anna! I usually use pumpkin fairly often in the fall, but not so much during the rest of the year!
Wow seems a healthy recipe
I have to try the receipt, looks super delicious. Thank you for sharing it with us.
Yum Yum Yum! I have to try these out! I’ve never been a pumpkin-lover, but these look too delish!
Hope that you liked them Danielle!
Wow! These sound and look really tasty! I especially appreciate your notes on the healthy ingredients. I’m always a big fan of using healthier options whenever possible!
Yes! I always try to substitute healthier ingredients. I find that I like most things even better when I do!
I love pumpkin spice anything! Those muffins look so yummy!
They are delicious! My daughter just made last week them for the millionth time this month.