Gluten-Free Pumpkin Chocolate Chip Muffins

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These Gluten-Free Pumpkin Chocolate Chip Muffins are filled with warm, cozy spices, dark chocolate chips, and chopped pecans for a yummy fall-inspired treat!

the top view of a plate of pumpkin chocolate chip muffins sitting on a marble countertop next to 4 pumpkin muffins, one of which has been sliced open with a gold butter knife

When it comes to fall baking, are you team pumpkin, apple, or I-don’t-care-just-give-me-all-of-the-fall-things? I’m *almost* in that third camp (I mean, ALL things fall make me super happy), but when it really comes down to it, if it’s pumpkin vs. apple, I will choose pumpkin EVERY SINGLE TIME. Pumpkin curry, pumpkin soup, pumpkin lasagna rolls (yes, that’s a thing!), pumpkin spice overnight oats, banana pumpkin pie muffins – if pumpkin is in the title, you can bet your bottom dollar that it’s on my “to-make” list from September-November (I’m also not opposed to making “pumpkin season” a year-round thing, but that’s just me!). 

These pumpkin chocolate chip muffins fall into the must-make-RIGHT-now category, so grab the ingredients, get your oven preheated, and let’s get to it! 

Gluten-Free Pumpkin Muffin Ingredients

These pumpkin chocolate chip muffins require some pretty standard baking ingredients, plus a few fall-inspired ingredients. Here’s what you’ll need to add to your grocery list:

  • Flour – this recipe calls for 1 and ¾ cups of all-purpose or gluten-free flour. We love King Arthur’s Measure for Measure flour if you’re going gluten-free here. 
  • Baking Powder – you’ll also need 2 teaspoons of baking powder and…
  • Baking Soda – …a ½ teaspoon of baking soda.
  • Pumpkin Pie Spice – to give these muffins their classic pumpkin pie flavor, you’ll also need to add in 2 teaspoons pumpkin pie spice (YUM!) and…
  • Pumpkin Puree – …1 cup of pumpkin puree. When you’re buying your canned pumpkin, be sure that you purchase pureed pumpkin and not pumpkin pie filling (pumpkin should be the only ingredient).
  • Brown Sugar – we love the rich, caramel-y flavor that brown sugar adds to these muffins, but feel free to substitute for an equal amount of coconut or regular white sugar if needed. 
  • Eggs – you’ll also need 2 eggs,…
  • Vanilla Extract – …2 teaspoons of vanilla extract,…
  • Butter – …8 tablespoons of melted butter (coconut oil works great here too!),…
  • Milk – …and a ¼ cup of milk (whole milk, cashew, oat, or almond milk are all great options). 
  • Dark Chocolate Chips – toss in a ½ cup of dark chocolate chips – we love THESE for a dairy-free option, THESE for a sugar-free version, and THESE for good ole regular chocolate chips!
  • Chopped Pecans – to finish off these muffins, you’ll need a ½ cup of chopped pecans!

How to Make Gluten-Free Pumpkin Chocolate Chip Muffins 

These muffins are super easy, and *oh so delicious*! Here’s how you’ll whip these up:

  1. Prep – preheat the oven to 350 degrees F, and line 12 muffin tins with parchment paper or silicone baking cups.
  2. Whisk the Dry Ingredients Together – add the flour, baking powder, baking soda, pumpkin pie spice, and salt to a large bowl and whisk to combine.
  3. Add the Wet Ingredients – add the pumpkin, brown sugar, eggs, vanilla extract, and melted butter (or coconut oil) to the bowl and beat with a hand mixer for 1-2 minutes, until fully combined.
  4. Add the Milk, Chocolate Chips, and Pecans – mix the milk into the batter, then stir in the pecans and chocolate chips until evenly incorporated.
  5. Spoon Into Muffin Tins + Bake – spoon the batter into the muffin tins until they are 3/4 of the way full, then bake for 25-30 minutes, until the muffins are fully set and don't jiggle in the center + a toothpick inserted into the center of the muffin comes out clean. 
  6. Let Cool + Enjoy!

the side view of 10 pumpkin chocolate chip muffins all sitting on a marble surface

What is the best flour to use for gluten-free baking?

Everything that comes out of the Fed and Fit kitchen *is* gluten-free (though if your body tolerates gluten, regular all-purpose flour can be used in place of GF flour in our baked good recipes), so we definitely know the scoop on the best gluten-free flour out there. We always get GREAT results with King Arthur Measure for Measure flour, plus, it’s easy to find, affordable, and doesn’t yield a gritty end product (as many gluten-free flours do). If you can’t find King Arthur GF flour, we also really like Bob’s Red Mill 1-to-1 GF flour. An important thing to note, when shopping for gluten-free flour, make sure that the blend you pick contains xanthan gum, and if it doesn’t, be sure to add in a teaspoon yourself.

Can this be made egg-free?

It can! In fact, we tested a TON of different egg substitutes in several different baked goods, took all kinds of notes, and then laid it all out for you in this super helpful guide to egg-free baking. For muffins, we recommend subbing in plain Greek yogurt (¼ cup of yogurt per egg) – Greek yogurt made for fluffy and slightly crisp on the outside muffins that had a really delicious flavor and held together really well.

Ingredient Variations and Substitutions 

Though this recipe is divine as written, feel free to play with it, and make it your own! Here are a few variations that we think would be especially yummy:

  • Swap the Pecans – use walnuts or pumpkin seeds in place of pecans if you’d like – they’d both be really delicious!
  • Add Dried Cranberries – experiment with adding dried cranberries (or another dried fruit of choice) in place of the pecans or chocolate chips, or toss in some cranberries in addition to the other two to make muffins that are really loaded with goodies!

How to Enjoy Pumpkin Chocolate Chip Muffins

Not only do these pumpkin muffins make for an excellent grab-and-go breakfast option (especially when you’re craving a comforting breakfast in the form of a baked good!), but they also make for a great addition to your standard breakfast and even a pretty great snack! Here are our favorite ways to enjoy these little bites of fall goodness:

  • With Nut Butter – add a dollop of your favorite nut butter (almond, peanut, or cashew butter would all be delicious here) before enjoying for a breakfast or snack with a little bit extra “staying” power.
  • On Top of a Yogurt Bowl – crumble a muffin on top of a bowl of full-fat plain Greek yogurt (THIS is our favorite!), add a handful of blueberries, and a drizzle of nut butter + maple syrup for a really delicious, filling, probiotic-packed breakfast!
  • In Addition to a Savory Breakfast – pair a pumpkin muffin (or two!) with a couple of eggs, bacon (or sausage), and lemony kale for a great sweet, carby addition to your everyday savory breakfast.

the side view of a batch of pumpkin chocolate chip muffins sitting on a plate next to one muffin on the countertop that has been sliced in half with a gold butter knife

How long can I store these pumpkin muffins?

Not only are these muffins super easy to make, but they’re also really easy to store! Before packaging, let the muffins cool to room temperature, then pack them into an airtight container (these glass storage containers are our favorite!), and store them in the fridge. Enjoy your pumpkin muffins from the fridge, or zap them in the microwave for about 30 seconds to enjoy them warm!

How do you freeze and reheat muffins?

I LOVE that these muffins can be frozen + reheated! It makes it super easy to make a double batch and store a batch for later (because who doesn’t want instant access to delicious pumpkin chocolate chip muffins at any moment?!). In order to keep your muffins from freezing together, we recommend popping them in the freezer on a parchment paper-lined sheet pan for 3-4 hours before transferring them to a large freezer-friendly bag to store in the freezer until you’re ready to enjoy. To reheat, simply microwave your muffin for 1-2 minutes!    

We hope you enjoy this delicious, fall-inspired pumpkin chocolate chip muffin recipe as much as we do – keeping them stocked in the freezer is a must during this time of year! 

More Fall-Inspired Recipes

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Gluten-Free Pumpkin Chocolate Chip Muffins

the side view of a batch of pumpkin chocolate chip muffins sitting on a plate next to one muffin on the countertop that has been sliced in half with a gold butter knife

These pumpkin chocolate chip muffins are the perfect fall treat that are loaded with warm spices, plenty of pumpkin flavor, toasted pecans, and dark chocolate.

  • Author: Amber Goulden
  • Prep Time: 20 minutes
  • Cook Time: 30 minutes
  • Total Time: 50 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Method: Oven
Scale

Ingredients

  • 1 3/4 cups flour
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 2 teaspoons pumpkin pie spice
  • 1/2 teaspoon salt
  • 1 cup pumpkin
  • 3/4 cup brown sugar
  • 2 eggs
  • 2 teaspoons vanilla extract
  • 8 tablespoons butter or coconut oil, melted
  • 1/4 cup milk (whole milk or your favorite dairy-free option)
  • 1/2 cup dark chocolate chips
  • 1/2 cup chopped pecans

Instructions

  1. Preheat the oven to 350 F and line 12 muffin tins with parchment paper or silicone baking cups.
  2. Add the flour, baking powder, baking soda, pumpkin pie spice, and salt to a large bowl and whisk to combine.
  3. Add the pumpkin, brown sugar, eggs, vanilla extract, and melted butter to the bowl and beat with a mixer for 1-2 minutes, until fully combined.
  4. Mix the milk into the batter, then stir in the pecans and chocolate chips until evenly incorporated.
  5. Spoon the batter into the muffin tins until they are 3/4 of the way full, then bake for 25-30 minutes, until the muffins are fully set and don't jiggle in the center, and a toothpick inserted into the center of the muffin comes out clean. Let cool for about 20 minutes, then enjoy!

Keywords: pumpkin, gluten-free, muffins, chocolate chips

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  1. Laura Kathleen McQueen says:

    Wondering what kind of flour to use for these. The recipe just says “flour”, but doesn’t specify what type. I’m GF and tend to stay away from almond flour if I can. Would love to know if I could use tigernut or coconut flour. Thanks!

    1. Kathy says:

      Before the recipe in the body of the post she talks about what flours can work! Hope that helps!

    2. Brandi Schilhab says:

      Our favorite GF flour is King Arthur Measure for Measure!

  2. Carrie says:

    This recipe is amazing! Can you please tell me where I can find the nutrition information? Thanks!

    1. Brandi Schilhab says:

      I just added it to the bottom of the recipe card, Carrie! Enjoy!

    2. Carrie says:

      Thank you so much!

    3. Brandi Schilhab says:

      Of course!

  3. Hillary says:

    I loved these! SO moist and loved the nuts AND chocolate together!

    5.0 rating

    1. Brandi Schilhab says:

      Yay!! So glad you loved them, Hillary!

  4. Brooke says:

    These were the perfect pumpkin muffin! Made a double batch to freeze some for next week.

    1. Brandi Schilhab says:

      So glad you loved them, Brooke!!! Thank you for sharing this with us!