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 (270 grams) gluten-free measure-for-measure flour; 1 cup (90 grams) gluten-free rolled oats; 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 (180 grams) semisweet chocolate chips, plus more for garnish; 2 Tablespoons (12 grams) rolled oats, for garnish (optional)

There’s something so cozy about pumpkin and chocolate chips coming together in a muffin, right? This Gluten-Free Pumpkin Chocolate Chip Muffins Recipe is exactly that kind of bliss—soft, tender, and perfectly spiced, with every bite feeling like a little autumn hug. Plus, it’s totally gluten-free but never missing any of that hearty, homey 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’ve made a ton of gluten-free muffins over the years, and this pumpkin chocolate chip version has become my favorite fall indulgence. It’s moist, fluffy, and doesn’t rely on a bunch of complicated ingredients—plus, it’s so forgiving if you want to play around with flavors or swap things out.

Perfect Texture: The combination of gluten-free flour and rolled oats gives these muffins a tender crumb without being dense or gummy.
Rich Pumpkin Flavor: Using pure pumpkin puree and warm spices means the pumpkin really shines through, not masked by other flavors.
Chocolate Chip Joy: You get melty bursts of chocolate in every bite, which is just the right touch of sweetness without overpowering the pumpkin.
Simple & Versatile: Easily made ahead, frozen, or customized, this recipe adapts to your schedule and taste buds.

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

The magic in these muffins lives right in the ingredients. Every component adds flavor, texture, or moisture that perfectly balances the mix. I always recommend using quality gluten-free measure-for-measure flour and pure pumpkin puree—not pie filling—to get the best results.

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 mimics traditional flour, giving structure and a familiar crumb without gluten’s chewiness.
Gluten-free rolled oats: Adding oats boosts the texture with subtle chewiness and extra fiber; be sure they’re certified gluten-free if you’re sensitive.
Baking powder and baking soda: They work together to give the muffins rise and lift, making them fluffy and light.
Salt and warm spices (cinnamon, ginger, cloves): These deepen the flavor and take pumpkin muffins from ordinary to crave-worthy.
Pure pumpkin puree: The star ingredient that keeps the muffins moist and full of that classic pumpkin taste.
Orange juice: I love how this adds brightness and a subtle citrusy note that complements the sweetness and spices.
Pure maple syrup: It provides natural sweetness and enhances the pumpkin flavor without being too sugary.
Avocado oil or melted coconut oil: For moisture and a gentle richness without a strong flavor.
Large eggs: They bind everything together and add protein and structure.
Semisweet chocolate chips: The delicious pockets of melty chocolate throughout these muffins make each bite special.
Rolled oats (for garnish, optional): A final touch that adds a rustic look and a tiny extra crunch if you want it.

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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 experiment with adding chopped nuts or swapping maple syrup for honey when I have it on hand. You can easily swap out the semisweet chocolate chips for dairy-free versions too if you need to keep it vegan. The best part? This recipe is your canvas to personalize however you like—it’s very flexible.

Variation: I once added a handful of chopped pecans for some crunch—it was a lovely surprise! You could also fold in dried cranberries for a tart note that pairs beautifully with pumpkin.

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

Step 1: Prep and Combine Dry Ingredients

First things first, preheat your oven to 375°F (190°C). Line your 12-cup muffin pan with parchment paper liners—I find this makes clean-up a breeze and helps the muffins release easily. Then, in a medium bowl, whisk together your gluten-free flour, gluten-free oats, baking powder, baking soda, salt, and those warm spices: cinnamon, ginger, and cloves. Whisking them well ensures an even distribution so every muffin bursts with that cozy flavor.

Step 2: Mix the Wet Ingredients

In a large bowl, whisk the pumpkin puree, orange juice, pure maple syrup, avocado or coconut oil, and eggs together until smooth and well blended. The texture will look silky and vibrant—the pumpkin really shines here. This mixture adds moisture and sweetness that make these muffins just right.

Step 3: Combine Wet and Dry, Then Add Chocolate Chips

Pour the dry ingredients into the wet and gently stir until they’re almost combined—don’t overmix or the muffins might get tough. Fold in 1 cup of chocolate chips so you get that melty chocolate goodness in every bite. Here’s a little tip: if you can, let the batter rest for 30 to 60 minutes before baking. This gives the oats a chance to soak up moisture and create a lighter, fluffier texture. If you’re prepping ahead, I’ve even let the batter chill overnight with great results.

Step 4: Scoop, Garnish, and Bake

Use an ice cream scoop or a ¼ cup measuring cup to portion the batter evenly into your muffin liners. For a pretty finishing touch, sprinkle a few extra chocolate chips on top and a pinch of rolled oats if you like. Pop the pan in the oven and bake for 18-20 minutes until the muffins are golden and a toothpick inserted in the center comes out clean or with just a few moist crumbs. Let them cool in the pan for a couple of minutes before transferring to a wire rack to finish cooling.

Top Tip

From my experience, resting the batter is a game changer. It’s the step that elevates these muffins, making them fluffier and lighter without you having to add extra leavening agents or chemicals.

Patience Pays Off: Let your batter rest for at least 30 minutes before scooping. It really improves texture and flavor.
Oil Choice: I’ve tried both avocado and coconut oils; I prefer avocado oil because it doesn't add a coconut flavor, making the pumpkin taste purer.
Mix Lightly: Mix your batter just until the wet and dry ingredients combine. Overmixing can make the muffins dense.
Check Doneness: Ovens vary, so start checking muffins at 18 minutes to avoid overbaking and drying them out.

How to Serve Gluten-Free Pumpkin Chocolate Chip Muffins Recipe

Pumpkin Chocolate Chip Muffins - Serving Suggestion

Garnishes

For a cozy vibe, I often add a light dusting of cinnamon or a drizzle of maple syrup right before serving. Toasted pecan halves on top add a lovely crunch and make them feel extra special. When I’m feeling festive, a smear of cream cheese frosting makes these muffins irresistible.

Side Dishes

These muffins pair wonderfully with a hot cup of chai tea or fresh brewed coffee—perfect for starting the day or an afternoon treat. If you want a fuller breakfast, serve them alongside scrambled eggs or a simple fruit salad for balance.

Creative Ways to Present

I’ve taken these muffin trays to fall brunches and decorated muffin display platters with autumn leaves and small pumpkins for guests. Wrapping each muffin with a parchment square tied with twine adds a quaint touch, perfect for gifting or party favors.

Make Ahead and Storage

Storing Leftovers

I usually store leftover muffins in an airtight container at room temperature—they stay fresh for about 2 days. If your kitchen is warmer or more humid, I recommend placing the container in the fridge to keep the muffins from getting too soft.

Freezing

Freezing these muffins works like a charm! Just wrap them individually in plastic wrap or foil, then pop them in a freezer bag. They’ll keep beautifully for up to 2 months. When you’re ready to enjoy, thaw at room temperature or gently reheat.

Reheating

To warm muffins without drying them out, I microwave them for about 15 seconds or heat them in a 350°F oven wrapped in foil for 5-7 minutes. This brings back that just-baked softness every time.

Frequently Asked Questions:

Can I substitute the gluten-free flour with regular flour?

You absolutely can swap in regular all-purpose flour if you’re not gluten-sensitive; just use the same amount by weight. The texture might be a bit different—usually a little lighter—but these muffins still come out delicious!

What can I use instead of pumpkin puree?

If you don’t have pumpkin puree on hand, canned butternut squash or sweet potato puree can be excellent substitutes and will give a similar moist texture and sweet flavor profile.

How do I make these muffins dairy-free?

This recipe is mostly dairy-free already, but to ensure that, use dairy-free chocolate chips and choose coconut oil instead of avocado oil if you prefer. Both options keep the muffins moist without dairy.

Can I make mini muffins instead?

Definitely! You’ll just reduce the baking time to about 12-15 minutes, but keep an eye on them. Mini muffins make a great bite-sized snack and are great for parties or lunchboxes.

Final Thoughts

I hope you’ll give this Gluten-Free Pumpkin Chocolate Chip Muffins Recipe a try soon. It’s one of those recipes that feels like a little gift of comfort, no matter the time of year. Whether you’re baking up a batch for breakfast, snacks, or a festive get-together, these muffins bring warmth, ease, and a touch of indulgence to your kitchen. Trust me, once you make them, they’ll become a go-to in your gluten-free baking repertoire.