Name: Gluten-Free Pumpkin Chocolate Chip Muffins Recipe
Prep time: 10 min
Cook time: 20 min
Total time: 30 min
Cuisine: American
Ingredients: 2 1/4 cups gluten-free measure-for-measure flour (270 grams); 1 cup gluten-free rolled oats (90 grams); 2 teaspoons baking powder; 1/2 teaspoon baking soda; 1 teaspoon salt; 2 teaspoons ground cinnamon; 1 teaspoon ground ginger; 1/2 teaspoon ground cloves; 1 (15-ounce) can unsweetened pumpkin puree (not pie filling); 1 cup orange juice; 1/2 cup pure maple syrup; 1/4 cup avocado oil or melted coconut oil; 3 large eggs; 1 cup semisweet chocolate chips (180 grams), plus more for garnish; 2 tablespoons rolled oats (12 grams), for garnish (optional)

There’s something magical about the cozy scents of fall baking wafting through your kitchen, and these Gluten-Free Pumpkin Chocolate Chip Muffins Recipe really hit that sweet spot. Moist, spiced, and loaded with pockets of melty chocolate, these muffins are a real crowd-pleaser — plus, they’re totally gluten-free without skimping on flavor or texture.

A single golden-brown muffin with a slightly rough texture, studded with dark brown chocolate chips and topped with pale oat flakes, sits on a white round marble slab with a fluted white paper liner partially open around it. In the background, out of focus, there is another similar muffin on a white marbled surface and a white bowl filled with chocolate chips. Some scattered oat flakes and chocolate chips are visible on the white marbled surface, adding detail and depth. The lighting is soft and natural, highlighting the warm, inviting color of the muffin. photo taken with an iphone --ar 2:3 --v 7

Jump to:

Why You'll Love This Recipe
Ingredients & Why They Work
Make It Your Way
Step-by-Step: How I Make Gluten-Free Pumpkin Chocolate Chip Muffins Recipe
Top Tip
How to Serve Gluten-Free Pumpkin Chocolate Chip Muffins Recipe
Make Ahead and Storage
Frequently Asked Questions:
Final Thoughts
Gluten-Free Pumpkin Chocolate Chip Muffins Recipe

Why You'll Love This Recipe

I adore how this Gluten-Free Pumpkin Chocolate Chip Muffins Recipe combines nostalgic fall flavors with a gluten-free twist that’s wonderfully forgiving. Every muffin comes out tender, fluffy, and packed with just the right balance of spices and sweetness — it’s proof gluten-free baking can be this satisfying!

Perfect Texture: These muffins are moist and fluffy, not crumbly or dry like many gluten-free treats.
Natural Sweetness: Using maple syrup and ripe pumpkin gives a lovely depth without overpowering sugar.
Balanced Warm Spices: Cinnamon, ginger, and cloves bring that cozy fall vibe without being too strong.
Chocolate Chip Goodness: Melty chocolate chips baked in every bite make these irresistible to both kids and adults.

Several golden brown muffins with a rough top filled with dark chocolate chips are arranged on a wire cooling rack above a white marbled surface. Each muffin is in a white paper liner and sprinkled with a few rolled oats on top. One muffin in the foreground is fully visible, showing a soft textured surface dotted with chocolate chips and oat flakes. A few chocolate chips and oat flakes have fallen onto the white marbled surface near the muffins. The overall scene has warm tones and soft natural light. photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

What I love most about this muffin recipe is how the ingredients complement each other effortlessly to create a tender crumb and rich flavor — plus, it’s higher in fiber thanks to rolled oats, making it feel a bit more wholesome. Here are the key players:

Flat lay of gluten-free measure-for-measure flour in a small white ceramic bowl, gluten-free rolled oats in a small white ceramic bowl, a small white ceramic bowl with baking powder, a small white ceramic bowl with baking soda, a small white ceramic bowl with salt, a small white ceramic bowl with ground cinnamon, a small white ceramic bowl with ground ginger, a small white ceramic bowl with ground cloves, a small white ceramic bowl filled with smooth unsweetened pumpkin puree, a small white ceramic bowl with bright orange juice, a small white ceramic bowl with pure maple syrup, a small white ceramic bowl with clear pale avocado oil, three large whole uncracked brown eggs arranged symmetrically, a small white ceramic bowl filled with semisweet chocolate chips, and a small white ceramic bowl containing a few rolled oats for garnish, all placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Gluten-free measure-for-measure flour: This takes the guessing out of gluten-free baking and ensures a crumb that fills out nicely.
Gluten-free rolled oats: Adds texture, fiber, and a subtle nuttiness that works beautifully with pumpkin.
Baking powder & baking soda: These leavening agents give the muffins that lovely lift and fluffiness.
Warm spices (cinnamon, ginger, cloves): These spices balance pumpkin’s natural sweetness and enhance the cozy fall feel.
Unsweetened pumpkin puree: The star of the show! Use pure pumpkin, not pie filling, for the right flavor and moisture.
Orange juice: I love this addition; it adds brightness and moisture without extra sugar.
Pure maple syrup: A natural sweetener that pairs perfectly with pumpkin and spices.
Avocado oil or melted coconut oil: Healthy fats keep the muffins moist and tender without heaviness.
Eggs: They bind everything together and contribute to the structure.
Semisweet chocolate chips: The melty pockets of sweetness that make these muffins extra special.
Rolled oats (for garnish): Optional, but I love the rustic look and slight crunch on top.

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Note: You'll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

I like to keep this recipe pretty classic, but it’s super easy to tweak depending on what you have or prefer. I encourage you to play around a bit and make these muffins your own!

Variation: I’ve swapped the semisweet chocolate chips for white chocolate or chopped pecans to add crunch—both work beautifully and give it a fresh twist.
Dietary Swaps: Use coconut sugar instead of maple syrup for a lower glycemic option, or try flax eggs to make it vegan-friendly.
Seasonal Substitutions: For an autumnal twist, stir in some chopped dried cranberries or swap half the pumpkin for sweet potato purée.

Step-by-Step: How I Make Gluten-Free Pumpkin Chocolate Chip Muffins Recipe

Step 1: Preheat & Prep Your Muffin Pan

First thing, get your oven heating to 375°F. I find this temperature perfect for baking these muffins to a golden top without drying them out. Line your 12-cup muffin tin with parchment liners—trust me, this saves you so much cleanup and keeps the muffins intact when removing!

Step 2: Combine Dry Ingredients

In a medium bowl, whisk together your gluten-free flour, rolled oats, baking powder, baking soda, salt, and all those gorgeous warm spices. Mixing these dry ingredients well before adding the wet prevents clumps and helps distribute flavors evenly.

Step 3: Mix the Wet Ingredients

Grab a large bowl and whisk your pumpkin puree, orange juice, maple syrup, avocado oil, and eggs until smooth and fully combined. This mixture is wonderfully fragrant and velvety—if you taste it (I won’t judge!), you get a hint at how flavorful these muffins will be.

Step 4: Bring Wet and Dry Together

Add your dry mix into the wet, stirring gently until just combined. Then fold in one cup of chocolate chips. Be careful not to overmix here—some lumps are okay; they make your muffins tender and light.

Step 5: Let It Rest (Magic Moment)

This might be my favorite trick: letting the batter rest for 30-60 minutes before baking. It helps hydrate the oats and flours, resulting in lighter, fluffier muffins. If you have more time, chilling overnight is a game-changer for texture and flavor depth.

Step 6: Scoop and Bake

Using an ice cream scoop or a ¼ cup measure, portion the batter evenly into the muffin cups. Top each with a few extra chocolate chips and a sprinkle of rolled oats for that final touch of presentation and crunch your guests will admire. Bake for 18-20 minutes, until the tops are golden and a toothpick comes out clean or with a few moist crumbs.

Step 7: Cool and Enjoy

Give your muffins 1-2 minutes to settle in the tin before transferring them to a wire rack. This little pause helps them firm up so you don’t have a crumbly mess. Then, dive in warm or wait for them to cool; they’re delicious either way!

Top Tip

From my experiments baking these Gluten-Free Pumpkin Chocolate Chip Muffins Recipe, I’ve learned a few nuggets that really make a difference. Thought I’d share so you can breeze through any common pitfalls and enjoy success every time.

Don’t Skip the Batter Rest: I’ve baked these muffins straight away, but the texture magically improves if you wait 30 minutes or chill overnight.
Choose the Right Flour: Using a measure-for-measure gluten-free flour blend keeps the crumb tender rather than gritty or dense.
Avoid Overmixing: Stir just until combined; overmixing develops the oats’ starch and can make muffins gummy.
Muffin Tin Matters: Using a metal muffin pan yields a better crust and even baking compared to glass or silicone in my experience.

How to Serve Gluten-Free Pumpkin Chocolate Chip Muffins Recipe

Pumpkin Chocolate Chip Muffins - Serving Suggestion

Garnishes

I usually keep the garnishes simple — just a few extra chocolate chips and a sprinkle of oats on top before baking adds a lovely rustic flair and a little tasty crunch. If I serve these for guests, I might add a dusting of cinnamon sugar or drizzle with a thin maple glaze for extra yum.

Side Dishes

These muffins are fantastic with a hot cup of chai tea or coffee. For a brunch spread, I like pairing them with a fresh fruit salad or a dollop of Greek yogurt mixed with a spoonful of honey to balance out their sweetness.

Creative Ways to Present

For a festive fall party, I’ve arranged these muffins on a wooden platter surrounded by cinnamon sticks, mini pumpkins, and fresh autumn leaves—people love the seasonal vibe! You could also serve them warm in individual cupcake wrappers lined with parchment squares, tied with twine for a charming gift or brunch table centerpiece.

Make Ahead and Storage

Storing Leftovers

Once cooled completely, I store leftover gluten-free pumpkin chocolate chip muffins in an airtight container at room temperature. They stay fresh for about 1-2 days before I notice any drying out, but honestly, they rarely last that long in my house!

Freezing

Freezing these muffins works wonderfully. I wrap individual muffins tightly in plastic wrap and then place them all in a freezer-safe bag. They hold up well for up to 2 months — perfect for a quick grab-and-go breakfast or snack later on.

Reheating

To reheat, I pop frozen muffins into the microwave for about 20-30 seconds or into a low oven (around 300°F) for 8-10 minutes. This brings back their soft, pillowy texture and that just-baked warmth you want — especially with the chocolate chips all melty again.

Frequently Asked Questions:

Can I use canned pumpkin pie filling instead of pumpkin puree?

You want to use pure unsweetened pumpkin puree here, not the pie filling, because pie filling contains added sugars and spices which could throw off the flavor and sweetness balance of the muffins. Using pumpkin puree gives you control over the spices and sweetness.

What can I substitute for orange juice if I don’t have it?

If you don’t have orange juice on hand, you can substitute it with apple juice, pineapple juice, or even just water. The juice adds a subtle brightness and moisture, but these alternatives work just fine without compromising texture.

Are these muffins suitable for a vegan diet?

This recipe as written includes eggs, so it’s not vegan. However, you can make it vegan-friendly by replacing eggs with flax eggs (mix 1 tablespoon of ground flaxseed with 2.5 tablespoons water per egg, let sit until gelled), and using coconut oil instead of avocado oil for a more plant-based approach.

How do I prevent my gluten-free pumpkin muffins from being dense or dry?

Great question! The keys are using a good measure-for-measure gluten-free flour blend, not overmixing your batter, and allowing the batter to rest before baking. Also, making sure you don’t overbake them keeps the muffins moist. Letting the batter rest hydrates the oats and flours, leading to a lighter, fluffier muffin.

Final Thoughts

This Gluten-Free Pumpkin Chocolate Chip Muffins Recipe has become one of my go-to fall treats because it feels like a warm hug in muffin form. The balance of spices, pumpkin, and chocolate chips hits that sweet nostalgic note without the gluten headache. I truly hope you enjoy making — and eating! — these as much as I do. Give them a try, and I bet they’ll become a fast favorite in your home, too.