August 23, 2021

Healthy Pumpkin Chocolate Chip Muffins

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.

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

muffin ingredients

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.

batter with chocolate chips

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.

batter in muffin tin

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.

baked muffins in tin

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!

muffins on plate

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


Healthy Pumpkin Chocolate Chip Muffins

  • Author: Ashlea Carver
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 1x
  • Category: Breakfast
  • Method: baking
  • Cuisine: American
  • Diet: Gluten Free
  • Author: Ashlea Carver
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 1x
  • Category: Breakfast
  • Method: baking
  • Cuisine: American
  • Diet: Gluten Free



  1. Preheat oven to 350 degrees. 
  2. Add the pumpkin purée, Greek yogurt, eggs, and vanilla extract to a mixing bowl and stir until well combined. 
  3. Next, add in the brown sugar and stir until well mixed.
  4. Add in the oat flour, baking soda, and pumpkin pie spice and stir until well combined. Next, fold in the chocolate chips.
  5. Transfer the batter to a greased muffin tin. Fill each muffin well two-thirds of the way full.
  6. Bake the muffins at 350 degrees for 15 to 20 minutes or until a toothpick, placed in the center, comes out clean.
  7. Serve the muffins warm, straight out of the oven, or enjoy them the next day!

Keywords: healthy pumpkin chocolate chip muffins, pumpkin chocolate chip muffins, healthy pumpkin muffins, pumpkin 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.

This post contains affiliate links.

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  1. Excellent recipe. I was tempted to eat halloween candy and decided to whip up these healthy treats before temptation led me to the dark side! 😛 These muffins are the PERFECT consistency, fluffy and moist. Let’s just say I did make these treats EXTRA healthy so I wouldn’t feel eating 2 for breakfast. I swapped the brown sugar for Lankato Classic Monkfruit Sweetener (zero calories) and added in extra dark chocolate 72% Ghiradhelli chocolate chips. They definitely don’t taste as decadent (my fault for these swaps) but I am looking forward to adding some almond butter and drizzling some honey on top and devouring them for a guilt free breakfast tomorrow morning!

  2. I love your site! It’s so pleasing to browse and enjoy! Can’t wait to make these today with my toddler!

  3. These were so delicious! Definitely dessert for me. To make them for breakfast I would use a few less chocolate chips and less brown sugar. A new fall favorite for sure!

  4. Hi Ashlea,
    I stumbled across your recipe this morning while looking for a new pumpkin muffin recipe and I just wanted to say they turned out AH-mazing!! I made 24 mini muffins without chocolate chips and 11 minutes was perfect. I had batter leftover so I made two jumbo muffins with it and added chocolate chips… thank you for a new favorite! I love how fluffy and moist they are. Oh, I used nonfat Greek, 30 cal almond milk and a coconut sugar/chicory root blend. Still perfect!!

  5. I saw these on Insta and had to make them! They are SO GOOD! The texture is perfect, and I love the addition of the Greek yogurt for some protein. The whole family has enjoyed them. Thanks too for the link about making your own oat flour – so easy and handy! This one is a keeper.

  6. These muffins were SO GOOD. I subbed dark chocolate chunks for chocolate chips and the were amazing. Another great recipe by Ashlea!

    • I’m so glad you loved it, Alaysia! Thanks for taking the time to leave a review!

  7. I needed a healthy treat for a family member and I came across these. So delicious! I doubled the recipe and they came out great.

  8. So delicious and easy to make. My husband and I devoured these muffins for breakfast within 2 days!!!

  9. Great recipe! Love how these muffins came out. Delicious, flavorful and not too sweet, exactly how I like it! My 10-year old daughter proclaimed these were the best muffins she ever had. I froze half of the batch for busy week ahead. Perfect for school day breakfast or afternoon snack.

  10. Does the recipe make a dozen? I’m trying to figure out if I need to double it for a group of 7 people who may have 1-2 muffins each and I want a few leftovers to freeze.

  11. I made theses muffins twice now once with sweet potatoe instead and they were both delicious. I put buttercream frosting on the sweet potatoe ones and were sooo good. Froze well and were wonderful reheated!

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