Fall baking means warmth, spice, and everything nice and nothing brings that cozy feeling to your kitchen like Gluten Free Pumpkin Chocolate Chip Muffins. These muffins are moist, perfectly spiced, and bursting with rich chocolate chips in every bite. Whether you’re a seasoned baker or just love pumpkin season, this easy gluten-free muffin recipe is one you’ll come back to again and again. Today, I’m sharing my go-to version that’s just sweet enough, naturally gluten-free, and perfect for breakfast, snacks, or dessert.
You’ll also get tips, variations (like a crumb topping or dairy-free version), and smart storage ideas so your muffins stay fresh and fluffy.
Gluten Free Pumpkin Chocolate Chip Muffins
Equipment
- 12-cup muffin pan
- Paper muffin liners
- mixing bowls
- whisk
- measuring cups and spoons
- spatula
- wire cooling rack
Ingredients
- 1 3/4 cups gluten-free all-purpose flour (with xanthan gum)
- 1 tsp baking soda
- 1/2 tsp baking powder
- 1/2 tsp salt
- 1 tsp cinnamon
- 1/2 tsp ground ginger
- 1/4 tsp nutmeg
- 1/8 tsp ground cloves
- 2 large eggs
- 1 cup pumpkin purée (not pie filling)
- 1/2 cup brown sugar
- 1/4 cup maple syrup or honey
- 1/3 cup neutral oil (avocado or sunflower)
- 1/4 cup unsweetened milk (oat or almond preferred)
- 1 tsp vanilla extract
- 1/2–3/4 cup semi-sweet chocolate chips
Instructions
- Preheat oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
- In a medium bowl, whisk together the flour, baking soda, baking powder, salt, and spices.
- In a large bowl, whisk together the eggs, pumpkin purée, brown sugar, maple syrup, oil, milk, and vanilla until smooth.
- Slowly add the dry ingredients to the wet mixture. Stir until just combined—don’t overmix.
- Fold in the chocolate chips.
- Scoop the batter evenly into the muffin cups. Bake for 18–22 minutes or until a toothpick inserted comes out clean.
- Let muffins rest in the pan for 5 minutes, then cool completely on a wire rack.
Notes
Nutrition
Ingredients You’ll Need
Here’s everything you need for these muffins. Keep it simple, seasonal, and gluten-free:
Dry Ingredients
- 1¾ cups gluten-free all-purpose flour (with xanthan gum)
- 1 tsp baking soda
- ½ tsp baking powder
- ½ tsp salt
- 1 tsp cinnamon
- ½ tsp ground ginger
- ¼ tsp nutmeg
- ⅛ tsp ground cloves
Wet Ingredients
- 2 large eggs
- 1 cup pure pumpkin purée (not pie filling)
- ½ cup brown sugar
- ¼ cup maple syrup or honey
- ⅓ cup neutral oil (avocado or sunflower work great)
- ¼ cup unsweetened milk (oat or almond preferred)
- 1 tsp vanilla extract
Add-ins
- ½–¾ cup semi-sweet chocolate chips
Craving more fall-inspired bakes? Try my Gluten-Free Apple Crisp or these Mini Gluten-Free Vegan Apple Muffins.
Step-by-Step Instructions
- Prep: Preheat your oven to 350°F (175°C) and line a 12-cup muffin pan with paper liners.
- Dry Mix: In a medium bowl, whisk together the flour, baking soda, baking powder, salt, and spices.
- Wet Mix: In a large bowl, whisk together the eggs, pumpkin purée, brown sugar, maple syrup, oil, milk, and vanilla.
- Combine: Slowly add the dry mix to the wet ingredients. Stir until just combined don’t overmix.
- Add Chocolate: Fold in the chocolate chips.
- Bake: Scoop the batter evenly into the muffin cups. Bake for 18–22 minutes or until a toothpick comes out clean.
- Cool: Let muffins rest in the pan for 5 minutes, then cool fully on a wire rack.
Looking for another easy option? My One Bowl Gluten-Free Banana Bread is just as simple.
Tips for Muffin Success
- Don’t overmix the batter gentle stirring keeps muffins soft.
- Room temp ingredients help everything blend smoothly.
- Toss chocolate chips in a little flour before folding them in. This keeps them from sinking.
- Let them cool completely before storing, to prevent soggy bottoms.
Need more muffin inspo? Try these Gluten-Free Blueberry Muffins next time you’re baking for brunch.
Flavor Variations to Try
These muffins are great as-is, but feel free to switch things up:
- Dairy-Free Version: Use dairy-free chips and a plant-based milk.
- Streusel Topping: Mix 2 tbsp brown sugar, 1 tbsp gluten-free flour, and 1 tbsp oil or butter. Sprinkle before baking.
- Nutty Twist: Add chopped pecans or walnuts for crunch.
- Mini Muffins: Use a mini muffin tin and bake for 10–12 minutes.
Want more cozy desserts? You’ll love my Gluten-Free Chocolate Chocolate Chip Cookies too.
Storage and Make Ahead Tips
Room Temp: Store in an airtight container for up to 3 days.
Fridge: Lasts 5–6 days chilled, but warm before serving for best texture.
Freezer: Freeze in a zip-top bag for up to 2 months. Thaw at room temp or microwave for 20–30 seconds.
Make-Ahead Tip: Bake and freeze a batch to enjoy during busy mornings.
If you’re prepping for the week, don’t miss my Gluten-Free Dessert Recipes for more freezer-friendly ideas.
FAQs About Gluten Free Pumpkin Chocolate Chip Muffins
1. Can I make these muffins without eggs?
Yes! Substitute 2 flax eggs (2 tbsp ground flax + 6 tbsp water, let sit 5 min). Muffins may be slightly denser but still delicious.
2. Why are my gluten-free muffins gummy?
Overmixing or using too much liquid can cause gumminess. Use a flour blend with xanthan gum and measure ingredients carefully.
3. Can I use almond flour or coconut flour instead?
No, not in a 1:1 swap. These absorb moisture differently and need separate ratios. Stick with a gluten-free all-purpose blend for best results.
4. How do I keep my muffins moist for days?
Cool fully, then store in an airtight container with a paper towel on the bottom to absorb moisture and prevent sogginess.
Final Thoughts
Gluten Free Pumpkin Chocolate Chip Muffins are everything you want in a fall treat soft, spiced, and studded with melty chocolate chips. Whether you’re baking for a family breakfast or prepping snacks for the week, this recipe is a seasonal staple you’ll return to again and again.
And if you’re ready to keep baking, check out my Gluten-Free Carrot Cake Recipe for another classic with a gluten-free twist.