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About This Recipe
Need a quick breakfast on-the-go or afternoon snack? Try these delicious Healthy Pumpkin Chocolate Chip Muffins for one of your favorite fall recipes yet! These muffins are super easy to make and are made with quality, wholesome ingredients. They sweet, nutritious and absolutely delicious!
Just like my Banana Nut Protein Muffins or my Double Chocolate Chip Protein Muffins, these healthy pumpkin muffins are great for breakfast on-the-go, an afternoon snack or even dessert. This is also a great recipe to freeze so feel free to make a double batch and save some for later!
Wondering how these delicious pumpkin muffins are so moist without using butter or excess oil? The secret ingredients are the pumpkin and applesauce! These two ingredients work perfectly together to replace the natural moisture calorie-dense butter adds (plus it keeps them dairy-free!). Plus, you get all the extra benefits of pumpkin like fiber, vitamins and minerals. Kids and husbands-alike will have no idea these tasty muffins are lightened up and actually good for you!
These pumpkin oat muffins are also great because they’re gluten-free and dairy-free. Serve these muffins with a side of greek yogurt or add your favorite nut butter on top for a real treat! Not sure what to do with leftover pumpkin? Try one of my 15+ Healthy Pumpkin recipes that are perfect for this time of year.

Why You’ll Love These Healthy Chocolate Chip Pumpkin Muffins
- A cross between breakfast and dessert! These muffins are slightly sweet with gooey chocolate but still nutritious!
- Gluten-free and dairy-free!
- Made with wholesome, healthier ingredients you can feel good about eating!
- This delicious recipe is simple and easy to make! Ready to eat in just 30 minutes.
- Lightened up and less than 200 calories per muffin. The perfect fall breakfast!

- Pumpkin purée – Libby’s has the best orange color and pumpkin flavor! You can also use homemade pumpkin puree if you wish.
- Unsweetened applesauce
- Pure maple syrup – can also substitute for sugar-free pancake syrup if you want less sugar!
- Coconut oil – or oil of choice!
- Eggs
- Vanilla
- Oat flour
- Pumpkin pie spice – store-bought or homemade pumpkin spice works great!
- Baking essentials: baking powder, salt, and baking soda
- Mini chocolate chips – my favorite chocolate chips are Enjoy Life!

To make dairy-free: use dairy-free chocolate chips (my favorite are Enjoy Life!).
To make vegan: substitute the eggs for flax eggs.
How To Make
The full printable recipe is below, but let me walk you through the process so you know what to expect when you’re making it!

1. In a large mixing bowl, mix together the pumpkin, applesauce, syrup, coconut oil, eggs and vanilla.

2. In a small bowl, whisk together the flour, pumpkin pie spice, baking powder, salt and baking soda.

3. Add the dry ingredients to the wet ingredients and mix until combined.

4. Then fold in the chocolate chips.

5. Transfer batter to a greased muffin pan. Top with extra chocolate chips so they’re pretty!

6. Bake for 20-22 minutes at 350F, or until a toothpick inserted comes out mostly clean.
Store leftover muffins in an airtight container in the fridge for up to a week.
To freeze, allow muffins to cool completely then wrap muffins tightly in a freezer-safe bag and freeze for up to 3 months.
Helpful Tips!
- Do NOT over mix! Over mixing the batter can cause denser, gummy muffins instead of light and fluffy muffins like we all love! For the best results, be sure to mix the wet and dry ingredients until just combined and them softly fold in the dark chocolate chips.
- Let your eggs come to room temperature! Let your eggs sit our roughly 30 minutes before baking or place them in a bowl of warm water for 3-5 minutes before you using them.
- Use fresh baking soda and baking powder! Be sure to use baking powder that hasn’t been open for more than 3 months. I like to write the date on top of the can whenever I open a new one to ensure I know when to start fresh!

What can I use if I don’t have oat flour?
To make your own oat flour, just blend regular oats in a blender or food processor until they’re a flour-like consistency! You can also sub oat flour for all-purpose flour, white whole wheat flour, or 1:1 gluten-free flour like Bob’s Red Mill or King Arthur.
What’s the best kind of pumpkin to use for this healthy pumpkin muffin recipe?
I always recommend using Libby 100% pure pumpkin for any of my pumpkin treats! I think Libby has the best color, taste and texture. Also be sure you’re using pumpkin puree (where the only ingredient is pumpkin) not pumpkin pie filling.
Can I bake this chocolate chip pumpkin muffin recipe in a loaf pan instead of regular pumpkin muffins?
Sure! You can easily use a loaf pan to make a healthy, quick pumpkin bread. Just be sure to adjust the baking time as it will take longer for the bread to bake. You can check the bread with a toothpick and it’s done once the toothpick comes out mostly clean (the bread will finish baking in the hot pan once removed from the oven).
How do these muffins stay moist without butter or vegetable oil?
The combination of pumpkin and the unsweetened applesauce pair perfectly to make these muffins light and moist! They also help lightened up this recipe since we aren’t using butter which is high in fat and calories. Not only does the pumpkin help this recipe be lower in calories but you get the added benefits of pumpkin being a vegetable so there is added fiber, vitamins, minerals and antioxidants!
More Pumpkin Recipes You’ll Love For Pumpkin Season
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Healthy Chocolate Chip Pumpkin Muffins (Gluten-free)
Ingredients
- 1 cup pumpkin puree (240g) Libby’s has the best orange color!
- 1/4 cup unsweetened applesauce (60g) or banana or more pumpkin
- 1/4 cup pure maple syrup (60g)
- 1/4 cup coconut oil (60g) melted
- 2 large eggs
- 1 tsp vanilla extract
- 2 cups oat flour (240g)
- 1 Tbsp pumpkin pie spice
- 1.5 tsp baking powder
- 1/2 tsp EACH: salt and baking soda
- 1/3 cup mini chocolate chips
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Instructions
- Preheat the oven to 350 degrees F. Spray a muffin pan with cooking spray.
- In a large bowl, mix together the pumpkin, applesauce, syrup, coconut oil, eggs and vanilla.
- In a small bowl, whisk together the flour, pumpkin pie spice, baking powder, salt and baking soda.
- Add the dry ingredients to the wet ingredients and mix until combined. Then fold in the chocolate chips.
- Transfer batter to the prepared muffin pan. Top with extra chocolate chips so they’re pretty.
- Bake for 20-22 minutes, or until a toothpick inserted comes out mostly clean. Then enjoy!
Equipment
Notes
- Do NOT over mix! Over mixing the batter can cause denser, gummy muffins instead of light and fluffy muffins like we all love! For the best results, be sure to mix the wet and dry ingredients until just combined and them softly fold in the dark chocolate chips.
- Let your eggs come to room temperature! Let your eggs sit our roughly 30 minutes before baking or place them in a bowl of warm water for 3-5 minutes before you using them.
- Use fresh baking soda and baking powder! Be sure to use baking powder that hasn’t been open for more than 3 months. I like to write the date on top of the can whenever I open a new one to ensure I know when to start fresh!
Nutrition Information
Nutrition is hand-calculated and accurate. No autocalulations! However, note that values can vary based on the brands you use and if you substitute ingredients.