As the air turns crisp and the leaves begin to crunch underfoot, there’s something inherently comforting about embracing the flavors of fall—specifically, homemade Gluten Free Pumpkin Muffins. The warm spices and vibrant pumpkin perfectly balance the sweetness of coconut sugar and indulgent chocolate chips, crafting an irresistible treat that’s bound to brighten up your day. What makes these muffins even better? They’re packed with protein, making them a wholesome option that keeps you energized without the dreaded sugar crash. Plus, with a few simple swaps, you can tailor this recipe to suit your dietary needs! Ready to fill your kitchen with the delightful aroma of baking and fall spices? Let’s dive into this delicious recipe together!

Why are these muffins a must-try?
Wholesome Flavor: These Gluten Free Pumpkin Muffins deliver a cozy burst of fall flavor, with pumpkin puree and warm spices creating a delightful balance of sweetness and comfort.
Packed with Protein: Each muffin contains high protein, thanks to the collagen peptides, making them a satisfying choice for breakfast or a snack.
Versatile Options: Want to switch things up? Feel free to swap almond flour for the gluten-free flour or use honey instead of coconut sugar for a unique twist.
Crowd-Pleasing Treat: Perfect for gatherings, these muffins bring smiles to everyone’s faces, whether enjoyed at breakfast with a warm drink or as a cozy afternoon snack.
Effortless Baking: With straightforward steps, you’ll have a batch of delectable muffins ready in no time. Why not pair them with a splash of homemade Oatmilk Pumpkin Spice for the ultimate fall indulgence?
Storage Friendly: Make a double batch and store extras for quick breakfasts—these muffins stay fresh for up to 4 days, making meal prep a breeze!
Gluten Free Pumpkin Muffin Ingredients
For the Muffins
• Gluten Free 1-to-1 Flour – Creates the muffin’s structure while ensuring it remains gluten-free.
• Unflavored Collagen Peptides – Adds protein and improves the texture; can be substituted with an equal amount of flour (1.75 cups) for a vegetarian option.
• Pumpkin Pie Spice – Provides delicious warm autumn flavor.
• Baking Powder & Baking Soda – Essential for leavening, helping muffins rise beautifully.
• Kosher Salt – Enhances the overall flavor of the muffins.
• Pumpkin Puree – A moisture-rich source and pumpkin flavor, using a whole 15 oz can.
• Large Eggs – Acts as a binding agent to keep everything together.
• Coconut Sugar – Offers light sweetness without the sugar overload; can be swapped for maple syrup or date sugar for variation.
• Avocado Oil (or Melted Refined Coconut Oil) – Provides rich moisture and flavor.
• Vanilla Extract – Adds depth and enhances all flavors in the muffins.
• Paleo Chocolate Chips – Infuses the muffins with sweetness and adds a delightful chocolatey contrast.
Feel free to experiment with these Gluten Free Pumpkin Muffins to create the perfect treat that satisfies your taste buds!
Step‑by‑Step Instructions for Gluten Free Pumpkin Muffins
Step 1: Preheat the Oven
Begin by preheating your oven to 375°F (190°C). While the oven warms, prepare a muffin tin by lining it with paper liners or greasing it lightly with oil to prevent sticking. This ensures easy removal of your delicious Gluten Free Pumpkin Muffins once they are baked.
Step 2: Mix Dry Ingredients
In a spacious mixing bowl, whisk together the gluten free 1-to-1 flour, unflavored collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt. This combination will create the foundation for your muffins, providing structure and flavor. Be sure to incorporate the ingredients thoroughly until well combined, which should take about 1-2 minutes.
Step 3: Combine Wet Ingredients
In another bowl, combine the pumpkin puree, large eggs, coconut sugar, avocado oil, and vanilla extract. Whisk the mixture until it becomes smooth and creamy, ensuring that all ingredients are well blended. This step takes about 2-3 minutes and helps create a moist interior for your Gluten Free Pumpkin Muffins.
Step 4: Combine Mixtures
Gently pour the dry ingredients into the bowl with the wet ingredients, mixing them together with a spatula or spoon. Be cautious not to over-mix the batter; you want it to be combined with a few flour specks still visible. This method helps to keep your muffins light and fluffy, enhancing their texture.
Step 5: Fold in Chocolate Chips
Once the batter is combined, fold in the paleo chocolate chips using a light hand. Make sure the chocolate chips are evenly dispersed throughout the batter without over-stirring, as this can lead to dense muffins. The chocolate will add a delightful sweetness and a rich texture to your Gluten Free Pumpkin Muffins.
Step 6: Rest the Batter
Allow the muffin batter to rest for about 15 minutes in the bowl. This short resting period enhances the muffin’s texture, making them even more moist and fluffy when baked. While you’re waiting, you can set out your lined muffin tin and prepare any optional toppings, such as extra chocolate chips.
Step 7: Fill Muffin Tins
After the batter has rested, carefully distribute it evenly into the prepared muffin cavities, filling each cup about ¾ full. If desired, sprinkle additional chocolate chips on top of each filled cup for an extra touch of sweetness and visual appeal. Ensure each muffin cavity is filled equally for even baking.
Step 8: Bake & Cool
Place the muffin tin in the preheated oven and bake for 22-25 minutes. You’ll know they’re done when they are golden brown and a toothpick inserted in the center comes out clean, with just a few moist crumbs attached. Once baked, let the muffins cool in the tin for 15 minutes before transferring them to a wire rack to cool completely. Enjoy the delightful aroma of your homemade Gluten Free Pumpkin Muffins as they cool!

How to Store and Freeze Gluten Free Pumpkin Muffins
Room Temperature: Keep your muffins in an airtight container at room temperature for up to 4 days. This helps maintain their moisture and flavor.
Fridge: For extended freshness, store in the refrigerator in an airtight container for up to a week—perfect for meal prepping gluten free pumpkin muffins!
Freezer: Flash freeze on a tray for 2 hours, then transfer to an airtight container or freezer bag. They can be stored in the freezer for up to 3 months.
Reheating: To enjoy, simply microwave for 20-30 seconds or place in a preheated oven at 350°F (175°C) for about 10 minutes to regain that fresh-baked taste.
What to Serve with Gluten Free Pumpkin Muffins
Fall is here, and it’s the perfect time to create a cozy meal that tantalizes the senses with every bite.
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Warm Spiced Chai Latte: The comforting flavors of chai spices complement the pumpkin muffins, making every sip a lovely embrace of fall.
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Crispy Bacon or Turkey Bacon: The salty bite of crispy bacon juxtaposes beautifully with the sweet spices in the muffins, creating a delightful flavor contrast.
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Fresh Fruit Salad: A colorful mix of apples, pears, and citrus refreshes your palate, balancing the richness of the muffins while adding a vibrant crunch.
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Creamy Yogurt Parfait: Layer some Greek yogurt with nuts and honey; it’s a tangy counterpart that enhances the muffins’ sweetness and adds delightful creaminess.
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Maple Pecan Oatmeal: The nutty flavor and warmth of oatmeal fortified with maple syrup make for a hearty breakfast that pairs wonderfully with pumpkin delight.
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Homemade Apple Cider: A warm mug of spiced apple cider enhances the autumn experience and perfectly highlights the pumpkin muffins’ cozy spices.
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Chocolate Chip Cookie Dough Ice Cream: For those who crave a sweet treat, this creamy dessert offers rich decadence that complements the muffins’ pumpkin and chocolate flavors.
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Nutty Granola Bars: Chewy, nutty, and full of fiber, these bars are great for pairing with the muffins as a healthy snack or breakfast option.
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Herbal Tea: A soothing cup of herbal tea provides a light balance and floral notes that enhance the fall-inspired spices in your muffins.
Make Ahead Options
These Gluten Free Pumpkin Muffins are perfect for meal prep enthusiasts! You can prepare the dry ingredients up to 24 hours in advance by mixing the gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and salt, then storing them in an airtight container to preserve freshness. Additionally, you can mix the wet ingredients (pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla) and refrigerate them overnight. When you’re ready to bake, simply combine the prepped mixtures, allow the batter to rest for 15 minutes, fold in the chocolate chips, and bake as usual. This way, you’ll have delicious homemade muffins ready with minimal effort, just as warm and tasty as they should be!
Expert Tips for Gluten Free Pumpkin Muffins
Measure Accurately: Using a digital kitchen scale ensures that your ingredients are measured precisely, leading to the perfect muffin texture.
Avoid Overmixing: Gently combine the wet and dry ingredients just until mixed, as over-stirring can lead to dense and heavy gluten free pumpkin muffins. A few flour specks are okay!
Let Batter Rest: Allowing your muffin batter to rest for about 15 minutes enhances its texture, making your baked muffins even fluffier and more enjoyable.
Cool Completely: Be patient! Letting your muffins cool completely before storage keeps them moist for longer, ensuring they’re delicious when you’re ready to enjoy.
Freezing Tip: For later enjoyment, flash freeze your muffins on a tray for 2 hours before transferring them to an airtight container—perfect for quick snacks!
Gluten Free Pumpkin Muffins Variations
Feel free to let your creativity shine as you customize these delicious muffins to fit your palate and dietary needs!
- Dairy-Free: Replace collagen peptides with a plant-based protein powder to keep it dairy-free.
- Sugar-Free: Swap coconut sugar for your favorite sugar-free sweetener to reduce sugar intake without sacrificing taste.
- Nut-Free: Use sunflower seed butter as a replacement for avocado oil for a nut-free option that still adds richness.
- Spice It Up: Add a pinch of cayenne pepper or a bit of fresh ginger for a warming kick that complements the pumpkin perfectly.
- Pumpkin Chocolate Chip Delight: Use white chocolate chips instead of dark for a different twist that adds a creamy sweetness.
- Add Fruits: Mix in fresh blueberries or finely chopped apples for a fruity surprise in every bite. They bring a juicy burst of flavor!
- Soften Texture: If you prefer an even softer muffin, add a tablespoon of unsweetened applesauce to the wet mixture. This adds moisture and flavor!
- Flavor Booster: Infuse the batter with freshly grated orange zest to brighten up the pumpkin flavors and add a refreshing citrus note.
For even more pumpkin-inspired treats, check out these delightful options: warm up with some savory Pumpkin Cinnamon Roll muffins or indulge in a cozy snack with Soft Pumpkin Cookies. Happy baking!

Gluten Free Pumpkin Muffins Recipe FAQs
What should I look for when selecting pumpkin puree?
Absolutely! When selecting pumpkin puree, look for a can that lists 100% pumpkin with no additives or preservatives. I personally prefer organic varieties for better flavor. Check that the can is free from dents and the expiration date is fresh—this ensures a tasty base for your gluten free pumpkin muffins!
How should I store my gluten free pumpkin muffins for the best freshness?
For optimal freshness, store your muffins in an airtight container at room temperature for up to 4 days. If you’d like them to last longer, refrigerate them which can keep them fresh for about a week. Just make sure they cool completely before storing to retain their moistness!
Can I freeze gluten free pumpkin muffins, and how should I do it?
Certainly! To freeze your muffins, first, flash freeze them by placing them on a tray for about 2 hours until solid. After they are frozen, transfer them to an airtight container or a freezer bag. They can be kept in the freezer for up to 3 months. When you’re ready to enjoy them, simply microwave for 20-30 seconds or warm them in a preheated oven at 350°F (175°C) for about 10 minutes for that fresh-baked taste.
What if my gluten free pumpkin muffins turn out denser than expected?
Very likely, the culprit is overmixing the batter! It’s important to mix just until the ingredients are combined and leave a few flour specks. Additionally, make sure your baking powder and baking soda are fresh, as they’re crucial for leavening. If you find they’re still dense, consider substituting the collagen for a lighter flour or checking that you’re using the right amount of ingredients.
Are these muffins pet-friendly or suitable for anyone with allergies?
While these muffins are gluten-free and can be made dairy-free with simple swaps, they do contain eggs and chocolate chips, which are not advisable for pets. Additionally, if you have allergies to nuts or eggs, be careful with substitutions. Always double-check ingredients as some chocolate chips may contain dairy.

Gluten Free Pumpkin Muffins You'll Crave This Fall
Ingredients
Equipment
Method
- Preheat your oven to 375°F (190°C) and prepare a muffin tin with liners or oil.
- In a spacious bowl, whisk together the gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and salt.
- In another bowl, combine the pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla, whisk until smooth.
- Gently combine the dry ingredients with the wet ingredients, mixing until just combined.
- Fold in the chocolate chips gently into the batter.
- Allow the batter to rest for about 15 minutes.
- Distribute the batter evenly into the muffin tin, filling each cup about ¾ full.
- Bake in the preheated oven for 22-25 minutes or until a toothpick comes out clean.
- Allow muffins to cool in the tin for 15 minutes before transferring to a wire rack.

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