As the leaves turn and the air becomes crisp, there’s nothing quite like the aroma of fresh-baked treats wafting through the kitchen. Enter my Gluten Free Pumpkin Muffins, a delightful way to celebrate the flavors of fall! These healthy pumpkin muffins are not only gluten-free but also high in protein, thanks to the addition of collagen peptides. Each muffin boasts a tender, fluffy texture and a satisfying 7g of protein, making them a perfect option for a nourishing breakfast or an afternoon snack. Lightly sweetened with coconut sugar and packed with warm spices, they offer a wholesome twist on a seasonal favorite. So, are you ready to fill your home with that comforting pumpkin spice fragrance? Let’s dive into this delicious recipe!

Why are these muffins a must-try?
Healthy treats never tasted so good! These Gluten Free Pumpkin Muffins are not just packed with fall flavors but are also high in protein, addressing your craving for something wholesome. Moist and fluffy, they melt in your mouth, making them an ideal choice for breakfast or a snack. Versatile by nature, you can customize them with different mix-ins like nuts or chocolate chips, keeping things exciting. Plus, the simplicity of the recipe will have you baking in no time! For more tasty treats, check out these Low Calorie Muffins or indulge in Pumpkin Cheesecake Muffins for that extra special touch!
Gluten Free Pumpkin Muffin Ingredients
• Unleash the cozy fall flavors!
For the Muffins
- Gluten Free 1-to-1 Flour – Provides the structure for the muffins; you can substitute with regular all-purpose flour if gluten isn’t a concern.
- Unflavored Collagen Peptides – Adds protein and improves the texture; replace with more gluten-free flour (increase to 1.75 cups) for a vegetarian version.
- Pumpkin Pie Spice – Enhances the flavor with warm spices; if you don’t have it, use a mix of cinnamon and nutmeg instead.
- Baking Powder – Acts as a leavening agent to ensure your muffins rise perfectly.
- Baking Soda – Works harmoniously with baking powder for added lift.
- Kosher Salt – Balances sweetness and enhances the overall flavor profile.
- Pumpkin Puree (15 oz can) – The star ingredient that adds moisture and rich pumpkin flavor; use pure pumpkin puree, not pie filling.
- Large Eggs – Provides structure and moisture; crucial for binding the muffins.
- Coconut Sugar – A natural sweetener that offers a subtle sweetness without the sugar crash.
- Avocado Oil – Adds moisture and fat to keep the muffins tender; can be swapped with melted coconut oil if desired.
- Vanilla Extract – Brings depth and warmth to the flavor.
- Paleo Chocolate Chips (1 cup) – Optional yet delightful mix-in that gives a rich, sweet contrast to the pumpkin flavor.
Let’s get ready to bake these healthy pumpkin muffins that will fill your home with warmth and joy!
Step‑by‑Step Instructions for Gluten Free Pumpkin Muffins
Step 1: Preheat Oven
Begin by preheating your oven to 375°F (190°C). This allows the heat to circulate evenly, ensuring your gluten-free pumpkin muffins are perfectly baked. While waiting, line a muffin tin with paper liners to make removing the muffins easy once they’re done baking.
Step 2: Prepare Dry Ingredients
In a large mixing bowl, whisk together the gluten-free flour, unflavored collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt. This step is crucial for distributing the leavening agents evenly throughout the batter, ensuring that the muffins rise beautifully. Set this bowl aside and take a moment to appreciate the warm aroma of the spices.
Step 3: Mix Wet Ingredients
In a separate bowl, combine the pumpkin puree, large eggs, coconut sugar, avocado oil, and vanilla extract. Using a whisk, blend these ingredients until the mixture is completely smooth and well combined. The bright orange puree will add both color and moisture, promising delightful, flavorful gluten-free pumpkin muffins.
Step 4: Combine Ingredients
Pour the dry mixture into the wet mixture slowly, stirring gently until just combined. Be cautious not to over-mix; some streaks of flour should remain visible. This helps keep your muffins light and fluffy instead of dense. The charming pumpkin spice scents will fill your kitchen—how inviting!
Step 5: Add Chocolate Chips
Gently fold in the paleo chocolate chips, ensuring an even distribution throughout the batter. The chips will provide a sweet contrast to the warm pumpkin flavor, elevating your gluten-free pumpkin muffins to a whole new level of deliciousness.
Step 6: Rest
Allow the muffin batter to rest for about 15 minutes. This resting period is important as it helps hydrate the dry ingredients, leading to a better texture in your muffins. You can prepare any additional toppings or gather your beloved coffee while waiting.
Step 7: Fill Muffin Tin
Evenly divide the batter among the 12 muffin cavities in your prepared muffin tin. If you like, sprinkle some extra chocolate chips on top for an eye-catching finish. Aim to fill each cavity about three-quarters full to prevent overflow while baking.
Step 8: Bake
Place your muffin tin in the preheated oven and set a timer for 22-25 minutes. The gluten-free pumpkin muffins are done when a toothpick inserted into the center comes out clean. Enjoy the intoxicating smell wafting from your oven, signaling that sweetness is on the horizon!
Step 9: Cool
Once baked, remove the muffin tin from the oven and let it cool for about 15 minutes. After cooling slightly, transfer the muffins to a wire rack to cool completely. This step prevents sogginess and keeps your muffins light and airy, ready to be enjoyed!

Expert Tips for Gluten Free Pumpkin Muffins
- Measure Carefully: Accurate measurements are crucial for baking gluten-free pumpkin muffins. Use a digital scale for consistency and best results.
- Avoid Over-Mixing: To keep your muffins light and fluffy, mix the batter until just combined. Over-mixing can result in dense muffins.
- Let Batter Rest: Allow the batter to rest for 15 minutes before baking. This helps hydrate the dry ingredients and enhances the texture of your muffins.
- Cool Before Storage: Make sure to cool the muffins completely before storing them. This helps maintain their moisture and freshness.
- Flash Freeze Leftovers: If you want to save some muffins for later, freeze them individually for a couple of hours before transferring to an airtight container for longer storage.
What to Serve with Gluten Free Pumpkin Muffins
As the aroma of fresh-baked muffins fills your home, consider the delightful ways to create a complete meal experience.
- Creamy Yogurt: Adds a luscious creaminess that balances the muffins’ warm spices. Dollop some on the side for a satisfying snack.
- Fresh Fruit Salad: A vibrant medley of seasonal fruits like apples and pears provides a refreshing contrast to the muffins’ richness. Each bite brightens up your plate!
- Nut Butter Spread: Almond or peanut butter can elevate the flavor profile while boosting the protein content. Spread it generously for a delicious pairing!
- Spiced Chai Latte: A warm, aromatic drink that complements the pumpkin spice perfectly, making for an inviting breakfast or afternoon treat.
- Maple Syrup Drizzle: Enhance sweetness with a light drizzle of pure maple syrup on top for an extra indulgent touch.
- Whipped Coconut Cream: This dairy-free option adds a light, airy texture that plays well with the muffins’ dense form. Just a spoonful elevates every bite!
- Savory Cheese Platter: Pair with sharp cheddar or creamy goat cheese for a delightful contrast that showcases both sweet and savory notes.
- Chilled Ginger Tea: A soothing drink that not only aids digestion but also complements the warm spices, creating a well-rounded snack moment.
- Chocolate Milk: For the ultimate treat, serve with a glass of rich chocolate milk that echoes the chocolate chips baked inside. Perfect for the kids!
- Caramel Drizzle: Add a drizzle of vegan caramel sauce on top for an extra layer of sweetness and a treat that’s simply irresistible.
Make Ahead Options
These Gluten Free Pumpkin Muffins are perfect for meal prep enthusiasts! You can prepare the dry ingredients—gluten-free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and salt—up to 3 days in advance. Simply store them in an airtight container to maintain freshness. The wet ingredients, including pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla, can be mixed and refrigerated for up to 24 hours. When ready to bake, combine the dry and wet ingredients, fold in chocolate chips, and rest the batter for 15 minutes. This way, you’ll have delicious, freshly baked muffins ready without all the last-minute fuss, providing you restaurant-quality results with minimal effort!
How to Store and Freeze Gluten Free Pumpkin Muffins
Room Temperature: Store muffins in an airtight container at room temperature for up to 4 days to keep them moist and flavorful.
Fridge: For longer freshness, place the muffins in the fridge, where they’ll stay fresh for up to a week. Allow to come to room temperature before enjoying.
Freezer: Freeze cooled muffins for up to 3 months. Flash freeze them on a baking sheet for a couple of hours, then transfer to an airtight container or freezer bag for storage.
Reheating: To enjoy, reheat in the microwave for about 15-20 seconds, or warm in the oven at 350°F (175°C) for 5-10 minutes until heated through.
Gluten Free Pumpkin Muffins Variations & Substitutions
Feel free to let your creativity shine with these delightful variations—each one adds a unique twist to your pumpkin muffin experience!
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Sweet Potato Swap: Use sweet potato puree instead of pumpkin for a slightly different flavor profile. It adds a nice creaminess too!
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Nutty Crunch: Toss in a handful of chopped walnuts or pecans for a delightful, crunchy texture that complements the softness of the muffins. Their earthy richness pairs beautifully with the pumpkin.
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Cranberry Burst: Mix in dried cranberries or raisins for a sweet-tart surprise in every bite. The added chewy texture contrasts perfectly with the muffins’ fluffiness.
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Spicy Kick: For a bit of heat, add a pinch of cayenne pepper or chili powder to the dry ingredients. It can transform your warming pumpkin spice muffins into something daringly unique.
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Vegan Friendly: Replace eggs with flaxseed meal or chia seeds combined with water. This simple swap maintains the moisture and structure while keeping it plant-based.
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Choco-Lover’s Delight: Experiment with different flavored chocolate chips, like dark chocolate or even cinnamon-infused chips, to liven things up.
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Classic Variant: Omit the chocolate chips for a more traditional pumpkin muffin experience, bringing forth the warm pumpkin flavor without distraction.
These variations not only breathe new life into your muffins but also cater to different tastes and dietary needs. And for a delightful treat beyond muffins, consider trying these Soft Chewy Pumpkin Oatmeal Cookies with Maple Frosting or indulge in Pumpkin Cupcakes with Maple Cream Cheese Frosting. Happy baking!

Gluten Free Pumpkin Muffins Recipe FAQs
What type of pumpkin puree should I use?
Absolutely! Use pure pumpkin puree from a can, ensuring it’s labeled “pure” and not “pumpkin pie filling.” The latter contains added sugars and spices that can throw off the flavor of your muffins. If you’re feeling adventurous, you can also make your own by roasting fresh pumpkins and blending them until smooth.
How should I store the muffins to keep them fresh?
I recommend storing your gluten-free pumpkin muffins in an airtight container at room temperature for up to 4 days. If you want to keep them longer, place them in the refrigerator, where they will remain fresh for about a week. However, if you prefer them at room temperature, just allow them to come to that after taking them out of the fridge.
Can I freeze these muffins? What’s the best way to do it?
Yes, you can freeze your gluten-free pumpkin muffins for up to 3 months! Start by cooling them completely, then flash freeze them on a baking sheet for about 2 hours. Once they’re solid, transfer the muffins to an airtight container or a freezer bag. When you’re ready to enjoy one, simply reheat it for about 15-20 seconds in the microwave or warm it in the oven at 350°F (175°C) for 5-10 minutes.
What to do if my muffins come out dense or dry?
Mixing the batter too much can lead to dense muffins, so be sure to mix until just combined—some flour streaks should be visible when you stop. If they come out dry, it might be a sign that your oven temperature was too high or you baked them for too long. Always keep an eye on them during the last few minutes of baking for the best results.
Are these muffins suitable for anyone with gluten allergies?
Yes! These gluten-free pumpkin muffins are created with gluten-free flour, making them safe for individuals with gluten intolerances or celiac disease. However, always check labels when using processed ingredients like baking powder and chocolate chips, as they can sometimes contain gluten.

Delicious Gluten Free Pumpkin Muffins Packed with Protein
Ingredients
Equipment
Method
- Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners.
- In a large bowl, whisk together the gluten-free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt.
- In another bowl, combine the pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla extract. Whisk until smooth.
- Pour the dry ingredients into the wet mixture slowly, stirring gently until just combined.
- Fold in the chocolate chips gently.
- Let the batter rest for about 15 minutes.
- Divide the batter among the 12 muffin cavities, filling each about three-quarters full.
- Bake for 22-25 minutes, until a toothpick comes out clean.
- Cool for about 15 minutes before transferring muffins to a wire rack.

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