These healthy pumpkin muffins with applesauce have a great flavor, the perfect amount of sweetness, and a nice, soft texture. They’re nutritious, too, with a little extra protein thanks to whole wheat pastry flour, eggs, and Greek yogurt! The perfect fall snack or portable breakfast. Plus, you can easily make this recipe into a loaf of healthy pumpkin bread if you prefer!
Autumn means crunchy leaves, apple cider, and of course pumpkin! There’s no denying pumpkin is a crazy popular flavor, especially during this time of year. And for good reason: it’s comforting, nutritious, and so tasty! So I’m excited to share one of my favorite fall-inspired pumpkin recipes with you. We love baking these pumpkin muffins (or the bread version) every fall!

Want to save this post?
Enter your email below and get it sent straight to your inbox. Plus, I’ll send you great content every week!
Yogurt Pumpkin Muffins
These pumpkin muffins are lightened up, but just as comforting as traditional muffins. I love when they’re baking and the pumpkin spice smell fills the house. Totally puts me in a cozy autumn mood!
The great thing about this recipe is that it’s versatile. You can add whatever you like (chopped nuts, shredded coconut, dried fruit) and it will still taste amazing! And, if you’d rather make bread instead of muffins, I’ve also included the instructions for that below.
Recipe Ingredients
To make this healthy pumpkin muffin recipe, you’ll need:
- Dry ingredients:
- whole wheat pastry flour
- brown sugar
- cinnamon
- pumpkin pie spice
- salt
- baking soda
- Wet ingredients:
- canned pumpkin puree
- raisins (or chocolate chips, pecans, walnuts, dried cranberries – whatever mix-ins your heart desires!)
- vanilla Greek yogurt
- unsweetened applesauce
- eggs
Greek yogurt and applesauce replaces the need for butter or oil, lightening up the muffins while keeping that soft texture intact. Need to make this recipe dairy-free? You can use a dairy free yogurt, like coconut yogurt or soy yogurt.
Be sure to use whole wheat PASTRY flour (or white whole wheat flour), not regular whole wheat flour. Otherwise, these will come out tough or too dense.
If you don’t have pumpkin pie spice, you can make your own! To make homemade pumpkin pie spice, just mix together 1 teaspoon ground cinnamon, 1/4 teaspoon ground ginger, 1/4 teaspoon ground nutmeg, and 1/8 teaspoon ground cloves.
If you have extra applesauce, try these healthy banana applesauce bars or these cinnamon apple crumble muffins, too!
How to Make Pumpkin Muffins with Applesauce
Per my usual standard, this recipe comes together quickly!
Start by preheating your oven to 350 degrees Fahrenheit. Next, mix the dry and the wet ingredients in separate bowls with a whisk.

Then, gently fold the wet ingredients into the dry ingredients in one bowl.

Stir until the mixture is mostly uniform, with no noticeable lumps. (Don’t over-mix the batter!).

Next, spoon the batter into a non-stick or greased muffin tin. You can also use muffin liners for easier cleanup. (If making bread, pour into a loaf pan.) Bake muffins for 25 minutes, or bread for 75 minutes. (This is when your kitchen will start to smell amazing! Want to make them a little extra pretty? Sprinkle some oats on top before baking!).
Take the muffins/bread out of the oven and check for done-ness with a fork or toothpick. If it doesn’t come out clean, bake a little while longer.

Then it’s time to enjoy. 🙂 They’re amazing as-is, or you can smear some yogurt or nut butter on top. For a little extra sweetness, drizzle some honey or maple syrup on them. They’re amazing with coffee, too! The ultimate autumn breakfast, snack, or healthy fall dessert. 🙂
Storage Tips
Store leftover muffins at room temperature in an airtight container for up to 3-4 days. Because they have a lot of moisture, it’s best to add a paper towel inside the container to help capture any excess moisture. This helps keep them from getting sticky or soggy! (I don’t recommend putting muffins in the fridge, because it can dry them out.)
The full recipe for pumpkin muffins with applesauce is at the bottom of this post. I hope you love them like I do!

For more delicious muffin/bread recipes, check these out:
And if you’re looking for more pumpkin recipe inspiration, I’ve got you covered:

Healthy Pumpkin Muffins with Applesauce & Greek Yogurt
These Healthy Pumpkin Muffins have a great flavor, the perfect amount of sweetness, and a nice, soft texture. Nutritious, too!
Ingredients:
Dry:
- 1.5 cups whole wheat pastry flour (or white whole wheat flour, or all-purpose flour)
- 1/2 cup brown sugar
- 1 teaspoon cinnamon
- 1 teaspoon pumpkin pie spice
- 1 teaspoon salt
- 1/2 teaspoon baking soda
Wet:
- 1 cup canned pumpkin
- 1/2 cup raisins (or chocolate chips)
- 1/4 cup vanilla Greek yogurt
- 1/4 cup unsweetened applesauce
- 2 eggs
Instructions:
Preheat oven to 350.
- In two separate bowls, mix dry, then wet, and then combine, adding wet to dry and stirring gently until the mixture is uniform-ish.
- Depending if you are making bread or muffins, either spoon the mixture into a non-stick (or greased) muffin tray or bread pan.
- Pop them in the oven for about 25 minutes (for muffins) or 75 minutes (for bread) and do a fork check near the end to test done-ness.

