The scent of warm pumpkin spice floating through the kitchen hits differently in October. My little one was painting ghosts on the windows while these muffins rose in the oven, and the moment I pulled them out, we both leaned in — noses first, then hands. Soft, chocolate-studded, and totally gluten free, they didn’t last long.
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Why You’ll Love These Gluten Free Pumpkin Muffins
These gluten free pumpkin muffins check so many boxes. They’re soft, lightly spiced, and crammed with chocolate chips in every bite. Also, they’re high in protein thanks to collagen peptides — a sneaky addition that doesn’t mess with the flavor or texture.
Each batch uses a full can of pumpkin puree, so no leftovers to store. They’re naturally gluten free, refined sugar free, and they hold together beautifully without feeling dense or dry. Whether you’re prepping ahead for the week or baking for a cozy fall morning, these muffins deliver every time.
Plus, they’re easy to customize and even easier to freeze for later. You’ll love how effortlessly they become part of your weekly routine.
Ingredients You’ll Need
These muffins come together with pantry staples and just one mixing bowl per step. Let’s break it down:
Dry Ingredients
- Gluten Free 1-to-1 Flour (1¼ cup): Choose a reliable blend like Bob’s Red Mill or King Arthur. Make sure it includes xanthan gum.
- Unflavored Collagen Peptides (½ cup): Adds protein without taste. If you’re vegetarian, just swap this with more gluten free flour (for a total of 1¾ cups).
- Pumpkin Pie Spice (1 tbsp): Gives that warm, cozy fall flavor.
- Baking Powder (1 tsp) + Baking Soda (¼ tsp): For lift and fluffiness.
- Kosher Salt (½ tsp): Balances sweetness and brings out the spice.
Wet Ingredients
- Pumpkin Puree (15 oz can): Be sure it’s plain pumpkin, not pie filling.
- Pasture-Raised Eggs (2 large): Helps bind and structure the muffins.
- Coconut Sugar (½ cup): A more natural sweetener with caramel notes.
- Avocado or Coconut Oil (¼ cup): Moisture without overpowering flavor.
- Vanilla Extract (1 tsp): Rounds out all the warm flavors.
Mix-ins
- Paleo Chocolate Chips (1 cup): I love the Hu brand, but use what you like. Mini or regular chips both work.
- Optional: Add chopped pecans or walnuts for crunch.
How to Make Gluten Free Pumpkin Muffins
These muffins don’t need any fancy steps. Here’s the simple process:
- Preheat your oven to 375°F. Line your muffin tin with paper liners. Spray them lightly if you want to prevent sticking.
- In a large bowl, whisk all your dry ingredients until fully combined.
- In a separate bowl, whisk together the wet ingredients until smooth and creamy.
- Add dry to wet. Stir until some streaks of flour remain — that’s key for tender muffins.
- Fold in the chocolate chips gently. Mix just until the flour disappears. Do not overmix.
- Let the batter rest for 15 minutes. This helps the muffins rise better and improves the texture.
- Scoop the batter evenly into the muffin cups. Sprinkle a few extra chips on top.
- Bake for 22–25 minutes, until a toothpick comes out with a few moist crumbs.
- Let them cool in the pan for 15 minutes, then transfer to a rack to cool completely.
Tips for the Best Pumpkin Muffins
- Use a scale if you can. Accuracy matters with gluten free baking. If not, spoon and level your flour.
- Avoid overmixing the batter. That’s the fastest way to end up with dense muffins.
- Check doneness with a toothpick — it should have a few moist crumbs, not wet batter.
- Store at room temp for up to 4 days in an airtight container. They stay moist and tender.
- To freeze, place cooled muffins on a tray to flash freeze, then store in a sealed container or bag. Reheat for 30–60 seconds in the microwave for a quick snack.
Gluten Free Pumpkin Muffins (Recipe Card)
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Gluten Free Pumpkin Muffins – Soft, Sweet & Protein-Packed
- Total Time: 50 minutes
- Yield: 12 muffins
- Diet: Gluten Free
Description
Soft, protein-rich gluten free pumpkin muffins made with real pumpkin, cozy spices, and paleo chocolate chips. Perfect for fall snacking or meal prep.
Ingredients
1¼ cup gluten free 1-to-1 flour (with xanthan gum)
½ cup unflavored collagen peptides (or use more flour for vegetarian)
1 tbsp pumpkin pie spice
1 tsp baking powder
¼ tsp baking soda
½ tsp kosher salt
1 can (15 oz) pumpkin puree
2 large eggs
½ cup coconut sugar
¼ cup avocado or melted refined coconut oil
1 tsp vanilla extract
1 cup paleo chocolate chips (plus extra for topping)
Instructions
1. Preheat oven to 375°F and line a muffin tin with liners (lightly spray if desired).
2. Whisk dry ingredients together in a large bowl.
3. In another bowl, whisk wet ingredients until smooth.
4. Add dry to wet and stir until some flour is still visible.
5. Fold in chocolate chips just until flour disappears. Do not overmix.
6. Let batter rest 15 minutes to improve rise and texture.
7. Divide batter into 12 muffin liners. Top with extra chocolate chips.
8. Bake for 22–25 minutes. Let cool in pan 15 minutes, then transfer to a rack.
Notes
Use a kitchen scale for best accuracy.
Do not substitute almond or coconut flour — they bake differently.
For vegetarian version: replace collagen with more flour (1¾ cups total).
Store in airtight container at room temp for up to 4 days.
To freeze: flash freeze then store in an airtight container. Reheat 30–60 sec.
- Prep Time: 10 minutes
- Cook Time: 25 minutes
- Category: Halloween Recipes
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 muffin
- Calories: 216
- Sugar: 13g
- Sodium: 199mg
- Fat: 11g
- Saturated Fat: 4g
- Unsaturated Fat: 5g
- Trans Fat: 0.003g
- Carbohydrates: 27g
- Fiber: 3g
- Protein: 7g
- Cholesterol: 27mg
More Such Recipes
If you love cozy, pumpkin-forward treats, check out these too:
Try pumpkin chocolate chip protein muffins for a nutritious snack.
Or whip up healthy pumpkin pancakes perfect for a fall breakfast.
Need a sweet treat? Bake soft pumpkin oatmeal cookies as a cozy gluten-free dessert.
And don’t miss pumpkin cottage cheese pancakes packed with protein for your morning meal prep.
Frequently Asked Questions
Can I make these muffins vegetarian?
Yes! Just replace the collagen peptides with more gluten free 1-to-1 flour. Your total flour will be 1¾ cups (or 218g). The texture will still be soft and moist.
Can I use almond flour or coconut flour instead?
Not for this recipe. Almond and coconut flour behave very differently and absorb moisture in unpredictable ways. They won’t yield the same structure or rise.
How do I store or freeze these muffins?
Keep them in an airtight container at room temperature for up to 4 days. To freeze, place them on a tray until solid, then store in a freezer bag or container. Reheat in the microwave for 30–60 seconds for a quick snack.
Final Thoughts
These gluten free pumpkin muffins are the kind of recipe that fits into real life. Whether you’re meal-prepping, baking with kids, or just craving something cozy, they deliver warmth, flavor, and a solid dose of protein.
If you make them, I’d love to hear how they turned out! Leave a comment or share a photo with me on Pinterest or Facebook. Happy baking, friend.