Moist, tender and fluffy, these gluten-free pumpkin chocolate chip muffins are an ideal fall bake — warm, spiced pumpkin batter studded with melty chocolate. They’re simple to make, naturally dairy-free, and perfect for breakfast or an afternoon snack.
Amazing Pumpkin and Chocolate Chip Muffins for Fall
These gluten-free pumpkin chocolate chip muffins combine classic autumn flavors with rich chocolate for a comforting treat. The combination of pumpkin puree, warming spices and chocolate chips creates a tender, flavorful muffin that’s great straight from the oven.
If you love pumpkin, this recipe will be one to bake often throughout the season.
Why You’ll Love this Recipe:
- Simple Ingredients: Most components are easy to find at any grocery store.
- Easy to Make: The recipe comes together quickly and yields a batch in under an hour.
- Gluten-Free & Dairy-Free: Made with gluten-free 1:1 flour and dairy-free chocolate and yogurt, these muffins suit many dietary needs while still tasting indulgent.
Ingredients You’ll Need:
Below is a photo overview of the main ingredients. Exact amounts are listed in the printable recipe card further down the page.
Recipe Notes + Substitutions:
- Pumpkin Puree: Use canned pumpkin puree or make your own. Do not substitute with pumpkin pie filling.
- Yogurt: Dairy-free plain yogurt keeps the muffins dairy-free; regular plain yogurt works if dairy is not a concern.
- Oil: Sunflower, canola, avocado or light olive oil all work well.
- Sugar: A mix of granulated and brown sugar gives good flavor; substitute with a 1:1 sweetener if desired for lower glycemic impact.
- Eggs: Eggs bind the batter—don’t omit unless using a tested egg replacer.
- Gluten-Free Flour: Use a quality gluten-free 1:1 blend made primarily from lighter flours and starches for a tender crumb. If you don’t need gluten-free, regular all-purpose flour can be used instead.
- Xanthan Gum: Add xanthan gum if your gluten-free blend doesn’t already include it to help the batter hold together.
- Spices: Cinnamon, nutmeg and ginger create classic pumpkin flavor. One can also use 2 teaspoons pumpkin pie spice.
- Chocolate: Use dairy-free chocolate to keep the recipe dairy-free; regular chocolate is fine if not avoiding dairy.
- Pumpkin Seeds: Optional for topping to add crunch and visual appeal.
How to Make Gluten-Free Pumpkin Chocolate Chip Muffins:
Combine Wet Ingredients and Sugar: In a large bowl, whisk together pumpkin puree, granulated sugar, brown sugar, vegetable oil, yogurt, eggs and vanilla until smooth.
Add Dry Ingredients: Add gluten-free 1:1 flour, xanthan gum (if needed), baking powder, baking soda and salt. Stir gently until just combined; avoid overmixing.
Prepare Chocolate Batter: Melt about 1/3 cup of the chopped chocolate and stir into half of the batter until smooth to create a chocolate portion.
Prepare Spiced Pumpkin Batter: To the remaining batter, add cinnamon, nutmeg and ginger, along with the remaining chopped chocolate and chocolate chips. Stir to combine.
Pour Batter into Muffin Cups: Line a muffin pan with paper liners. Alternate spoonfuls of the chocolate and pumpkin batters into the cups and use a toothpick or skewer to swirl for a marbled look.
Sprinkle and Bake: Top with pumpkin seeds and extra chocolate chips if you like.
Bake Until Ready: Bake at 350°F (175°C) for 25–30 minutes, or until a toothpick inserted in the center comes out clean.
Let Cool Before Enjoying: Transfer to a wire rack and let cool completely before serving for the best texture.
Tips and Variations:
- Toppings: Try shredded coconut, rolled oats or a sprinkle of cinnamon sugar instead of pumpkin seeds.
- Mix-Ins: Fold in chopped pecans or walnuts for extra texture.
- Cocoa Option: Swap melted chocolate for 2 tablespoons cocoa powder mixed into the batter for a different chocolate profile.
- Pan Sizes: This recipe yields 12 regular muffins. For mini muffins bake 15–20 minutes; for jumbo muffins bake 40–45 minutes, watching doneness.
- Storage: Store cooled muffins in an airtight container in the refrigerator up to 3 days; reheat briefly before serving.
- Freezing: Freeze cooled muffins in a freezer-safe bag or container for up to 2 months. Reheat from frozen until warm.
Other Gluten-Free Pumpkin Desserts to Love:
- Crustless Pumpkin Pie (Gluten-Free, Dairy-Free)
- Gluten-Free Pumpkin Scones (Dairy-Free)
- Chewy Pumpkin Cookies (Gluten-Free, Dairy-Free)
- Easy Pumpkin Waffles (Gluten-Free, Dairy-Free)
Other Gluten-Free Muffins to Bake:
-
Almond Flour Blueberry Muffins (Gluten-Free, Dairy-Free)
-
Almond Flour Chocolate Chip Muffins (Gluten-Free, Dairy-Free)
-
Gluten-Free Cranberry Orange Muffins (Dairy-Free)
-
Gluten-Free Pumpkin Banana Muffins (Dairy-Free)
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Gluten-Free Pumpkin Chocolate Chip Muffins (Dairy-Free)
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- Author: Felicia Lim
- Total Time: 45 minutes
- Yield: 12 muffins
- Diet: Gluten Free
Description
Moist, tender and fluffy, these gluten-free pumpkin chocolate chip muffins are the perfect fall snack — warm, spiced and studded with chocolate. They’re dairy-free and easy to make.
Ingredients
Units
Scale
- 1 cup pumpkin puree
- 1/2 cup plain dairy-free yogurt (or regular plain yogurt)
- 1/3 cup vegetable oil
- 1/2 cup granulated sugar
- 1/4 cup brown sugar
- 2 eggs
- 1 1/2 tsp ground cinnamon
- 1/4 tsp ground nutmeg
- 1/4 tsp ground ginger
- 1 tsp vanilla extract
- 1 3/4 cups gluten-free 1:1 flour (or all-purpose flour)
- 1/2 tsp xanthan gum (omit if your blend includes it)
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp salt
- 1/2 cup chopped dairy-free chocolate
- 1/2 cup dairy-free chocolate chips
- Pumpkin seeds (pepitas), for topping
Instructions
- Preheat & Line: Preheat oven to 350°F (175°C) and line a muffin pan with paper liners.
- Combine Wet Ingredients: Whisk pumpkin puree, granulated sugar, brown sugar, oil, yogurt, eggs and vanilla until smooth.
- Add Dry Ingredients: Stir in the gluten-free flour, xanthan gum (if needed), baking powder, baking soda and salt until just combined.
- Prepare Chocolate Batter: Melt 1/3 cup chopped chocolate and mix into half the batter until smooth.
- Prepare Spiced Batter: To the other half add cinnamon, nutmeg, ginger, remaining chopped chocolate and chocolate chips; stir to combine.
- Assemble: Spoon alternating portions of each batter into the muffin cups and swirl gently for a marbled effect.
- Top: Sprinkle with pumpkin seeds and extra chips if desired.
- Bake: Bake 25–30 minutes or until a toothpick comes out clean.
- Cool: Let the muffins cool completely on a wire rack before serving.
Notes
Pumpkin Puree: Use plain pumpkin puree, not pumpkin pie filling.
Flour: For a lighter texture, choose a gluten-free 1:1 blend made with rice flour and starches; regular all-purpose flour works when not gluten-free.
Xanthan Gum: Add only if your gluten-free blend lacks it.
Sugar & Oil: Swap sugars or oils as preferred; choose substitutes that match the original textures for best results.
Chocolate: Dairy-free chocolate keeps this recipe dairy-free; use regular chocolate if desired.
Storage: Refrigerate cooled muffins in an airtight container up to 3 days; freeze up to 2 months.
- Prep Time: 15 mins
- Cook Time: 30 mins
- Category: Muffins
- Method: Baking
- Cuisine: American