Healthy pumpkin chocolate chip muffins made with oat flour, pumpkin, and plain Greek yogurt for an extra punch of protein. These easy muffins are sweetened with a touch of brown sugar and have plenty of pumpkin pie spice for that perfect fall flavor.

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Healthy Pumpkin Chocolate Chip Muffins

Tis the season for all the fall treats which means…pumpkin chocolate chip muffins!

The combination of pumpkin and chocolate chips are a match made in heaven and these healthy pumpkin chocolate chip muffins are such a delicious treat. They are my FAVORITE.

With just the right amount of pumpkin pie spice, sweetness, and a pack of protein from Greek yogurt, these muffins make a delicious snack or afternoon treat.

Drizzle a little nut butter on top or add in your favorite nuts for a little more crunch.

Reader Favorite Pumpkin Recipes

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Gluten Free Pumpkin Chocolate Chip Muffin Ingredients

Note: full ingredients list & measurements provided in the Recipe Card, below.

Pumpkin Puree: Be sure to use pumpkin puree and not pumpkin pie filling. The only ingredient should be pumpkin.

Greek Yogurt: This helps to pack in a little extra protein into the muffins and keeps them moist.

Oat Flour: This flour is naturally gluten free and works well in these muffins. I’ve included instructions on how to make oat flour from scratch below.

Brown Sugar: You could also use coconut sugar if you prefer.

Pumpkin Pie Spice: For that delicious pumpkin spice flavor that we all love. If you’re out, feel free to make your own homemade pumpkin pie spice.

Chocolate Chips: Chocolate chips are always optional but they are absolutely perfect in these muffins. I prefer the flavor of dark chocolate but feel free to use milk chocolate if you prefer.

How to Make Oat Flour

These pumpkin muffins are naturally gluten-free thanks to one of my all-time favorite gluten-free flours to use when baking – oat flour. Gluten-free baking can be a little tricky and I’ve had my fair share of baking fails when experimenting with almond flour or coconut flour.

Thankfully, as long as you have gluten-free oats in your pantry, you can make a large batch of oat flour yourself, for pennies on the dollar, with a high-powered blender or food processor.

To make oat flour, just add a few cups of gluten-free oats to your food processor or blender. Pulse or blend until the oats completely break down and become the consistency of traditional flour. This process only takes a minute or so in my high-powered Vitamix and a few minutes in my food processor.

You can also watch this quick video for a step-by-step tutorial on how to make oat flour and all of my best tips.

How to Make Healthy Pumpkin Muffins with Chocolate Chips

Note: full ingredients list & measurements provided in the Recipe Card, below.

• Mix the wet ingredients. Add the pumpkin purée, Greek yogurt, eggs, brown sugar, and vanilla extract to a mixing bowl and whisk together until well combined.
• Add the dry ingredients. Next, stir in the sugar and then add the oat flour, baking soda, and pumpkin pie spice.
• Fold in the chocolate chips. Stir the chocolate chips into the batter until everything is well combined.
• Fill the muffin tin. Transfer the batter to a greased muffin and fill each muffin well two-thirds of the way full.
• Bake the muffins. 350 degrees for 15 to 20 minutes or until a toothpick comes out clean when inserted in the center.
• Serve warm. These muffins are delicious warm and straight out of the oven. I like to let them cool for just a few minutes before diving in.

How to Store, Freeze, and Reheat

You will need to store these muffins in the fridge to keep them fresh. If you do not think you’ll be able to eat all of the muffins within two to three days, you can easily store them in the freezer.

• To freeze the muffins: let them come to a complete cool on a wire baking rack. Once they are cool, place them in a freezer safe storage bag or container. Label the container or bag with the date and you are all set.
• To reheat a muffin: you can do so in one of two ways – My preferred method is to wrap one or two muffins in foil and let them reheat in a 350 degree oven for approximately ten minutes until they are warmed through fully. The muffins will taste just like a fresh batch. If you are short on time, you can take a muffin straight from the freezer and place it in the microwave for thirty seconds to reheat.

Tips and Tricks

• To ensure that your muffins do not stick, be sure to well grease or line your muffin tin with cupcake liners.
• If you are out of pumpkin pie spice and don’t have the spices to make your own, you can use one teaspoon of cinnamon instead.
• Don’t love chocolate? Feel free to leave the chocolate chips out altogether or replace them with chopped pecans.

Frequently Asked Questions

Can I use almond flour or coconut flour?

No. Coconut flour or almond flour will not work as a substitute for oat flour in this recipe. While I have not tested it, what will likely work best is all purpose flour.

Can I make these muffins dairy free?

Yes! Feel free to use your favorite dairy free Greek yogurt in this recipe to ensure the muffins are dairy free. Be sure to use dairy free chocolate chips as well!

More Delicious Recipes to Love

Healthy Almond Butter Sweet Potato Muffins

Gluten Free Apple Cinnamon Muffins

Healthy Banana Chocolate Chip Muffins

Gluten Free Brown Butter Banana Muffins

Recipe by: Ashlea Carver / All the Healthy Things | Photography by: Casey Colodny / THE MINDFUL HAPA

This post was originally published on October 27, 2020 and republished on August 24, 2021.