Gluten Free Pumpkin Muffins bring the perfect blend of fall flavors with a healthy twist. These moist, fluffy muffins are made with wholesome ingredients like pumpkin puree and paleo chocolate chips, making them naturally dairy-free and high in protein. Whether you’re looking for a healthy pumpkin muffin recipe or a simple fall baking recipe, these muffins are the ideal treat for cozy mornings or meal prep. Easy to make, deliciously moist, and nutritious this recipe is a must-try for pumpkin lovers!
Why You’ll Love These Healthy Gluten Free Pumpkin Muffins
These gluten free pumpkin muffins are the perfect fall treat, offering all the cozy flavors of the season in a healthier package. Whether you’re indulging in a quick breakfast or satisfying your sweet tooth, these muffins check all the boxes. Here’s why:
- Moist & Fluffy Texture: Thanks to the pumpkin puree, each bite delivers a soft, melt-in-your-mouth texture. The addition of avocado oil helps keep them tender while ensuring they remain light and airy no dense, dry muffins here!
- High in Protein: With added unflavored collagen peptides, these muffins provide 7 grams of protein per muffin, making them a great way to start your day or refuel after a workout.
- Naturally Dairy-Free: Made without any dairy, these muffins are perfect for those with lactose intolerance or anyone following a dairy-free lifestyle.
- Paleo-Friendly: With paleo chocolate chips and gluten-free flour, they fit seamlessly into both paleo and gluten-free diets without sacrificing flavor.
- Healthy & Wholesome Ingredients: Sweetened lightly with coconut sugar, these muffins provide a naturally balanced sweetness that won’t spike your blood sugar.
These healthy pumpkin muffins are more than just a delicious treat they’re a nutritious way to enjoy fall baking. Whether you’re meal prepping for the week or serving them at your next brunch gathering, they’re guaranteed to be a hit with everyone.
Ingredients for the Best Pumpkin Muffins (with Paleo Chocolate Chips)

Creating the perfect batch of gluten free pumpkin muffins starts with the right ingredients. Here’s what you’ll need:
Dry Ingredients:
- 1 ¼ cups gluten free 1-to-1 flour (for the ideal texture without the gluten)
- ½ cup unflavored collagen peptides (adds protein without affecting taste or texture)
- 1 tbsp pumpkin pie spice (for that classic fall flavor)
- 1 tsp baking powder (for the perfect rise)
- ¼ tsp baking soda (works with the pumpkin puree to give the muffins the right fluff)
- ½ tsp kosher salt (enhances all the flavors)
Wet Ingredients:
- 1 can (15 oz) pumpkin puree (the star ingredient that keeps the muffins moist)
- 2 large eggs (adds structure and protein)
- ½ cup coconut sugar (a healthier, lightly sweet alternative to refined sugar)
- ¼ cup avocado oil (or melted refined coconut oil for a neutral flavor)
- 1 tsp vanilla extract (for a touch of sweetness and depth)
Mix-Ins:
- 1 cup paleo chocolate chips (adds a rich, melty sweetness without dairy or refined sugar)
These ingredients come together to create a perfect balance of flavor, texture, and nutrition. You won’t need any special tools just basic kitchen equipment like mixing bowls, a whisk, and a muffin tin. Plus, most of these ingredients are pantry staples, so you can whip up a batch whenever that pumpkin craving hits!
Step-by-Step: How to Make Moist Gluten Free Pumpkin Muffins
Making these gluten free pumpkin muffins is quick and easy, and with just a few simple steps, you’ll have a batch of fluffy, moist muffins ready to enjoy. Follow these instructions for the best results:
- Preheat your oven and prepare your muffin tin:
Preheat the oven to 375°F (190°C). Line a muffin tin with paper liners or grease the tin to ensure easy removal once baked. - Mix the dry ingredients:
In a large bowl, whisk together the gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt. Ensure everything is well-combined for an even texture. - Combine the wet ingredients:
In another bowl, whisk together the pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla extract until smooth. Make sure there are no lumps from the pumpkin puree. - Add the dry ingredients to the wet ingredients:
Gradually pour the dry ingredients into the wet mixture, stirring gently with a spatula. Mix until the batter is mostly combined but don’t overwork it — a few lumps are okay. - Fold in the chocolate chips:
Gently fold in the paleo chocolate chips using a spatula, ensuring they are evenly distributed throughout the batter. - Rest the batter:
Let the batter rest for 10–15 minutes. This step allows the flour to absorb the wet ingredients and helps the muffins rise better. - Fill the muffin tin and bake:
Divide the batter evenly among the 12 muffin cavities, filling each about 2/3 full. Bake for 22–25 minutes, or until a toothpick inserted into the center comes out clean with just a few moist crumbs attached. - Cool and enjoy:
Let the muffins cool in the tin for about 10 minutes, then transfer them to a wire rack to cool completely. Enjoy them fresh, or store for later!

Expert Baking Tips for Perfectly Fluffy Texture
To ensure your gluten free pumpkin muffins turn out perfectly every time, follow these expert tips for a moist, fluffy texture:
- Don’t Overmix the Batter:
When combining the wet and dry ingredients, stir just until everything is incorporated. Overmixing can cause the muffins to become dense and dry. A few lumps in the batter are perfectly fine! - Let the Batter Rest:
Allow the batter to sit for 10–15 minutes before scooping it into the muffin tin. This helps the gluten free flour fully absorb the wet ingredients, leading to a better rise and fluffier texture. - Use a Kitchen Scale for Accuracy:
For the most accurate measurements, especially with gluten free flour, use a kitchen scale. Gluten-free baking can be finicky, and a slight difference in ingredient amounts can affect the texture. - Check Muffin Doneness with a Toothpick:
At 22 minutes of baking, use a toothpick to check the center of a muffin. If it comes out clean or with just a few moist crumbs, they’re ready. If the toothpick comes out wet, bake for another 2–3 minutes. - Don’t Skip the Cooling Time:
Let the muffins cool in the tin for about 10 minutes before transferring them to a wire rack. This helps them set and prevents them from falling apart. The muffins will continue cooking slightly as they cool.
By following these simple tips, you’ll ensure that your muffins come out light, fluffy, and perfectly textured every time.
ubstitutions & Variations for Dairy-Free or Paleo Baking
This gluten free pumpkin muffin recipe is already tailored for many dietary needs, but if you’re looking to tweak it to suit your preferences or dietary restrictions, here are a few substitution options:
For a Vegan Version:
- Eggs: Replace the 2 large eggs with flax eggs (1 tablespoon of ground flaxseed mixed with 2.5 tablespoons of water for each egg). Let the mixture sit for 5 minutes before using to allow it to thicken.
- Coconut Sugar: If you want a lower glycemic index, you can swap the coconut sugar for stevia or another low-sugar sweetener. Just be sure to adjust the amount according to the sweetness level of your chosen substitute.
For a Grain-Free Option:
- Flour: If you prefer a grain-free option, you can substitute the gluten free 1-to-1 flour with almond flour. Keep in mind that you might need to adjust the quantity, as almond flour behaves differently from gluten-free flour blends.
- Baking Powder: Ensure your baking powder is also grain-free (some contain cornstarch, which is not allowed in paleo diets).
For Extra Protein:
- Collagen Peptides: To boost the protein content, you can increase the amount of unflavored collagen peptides. You can also add a scoop of plant-based protein powder for an even higher protein muffin, though this might affect the texture slightly.
For a Nut-Free Version:
- If you’re looking to keep the muffins nut-free, ensure you’re using a nut-free flour blend (like the 1-to-1 gluten-free flour) and avoid any nut-based add-ins. Instead, you could add sunflower seeds or pumpkin seeds for a bit of crunch.
For Extra Flavor Variations:
- Add-ins: Spice things up by adding a handful of raisins, dried cranberries, or chopped nuts (like pecans or walnuts) to the batter for extra texture and flavor.
- Spices: You can also experiment with different spice blends, such as cinnamon, nutmeg, or even ginger, depending on your taste preference.
These simple swaps allow you to personalize this gluten free pumpkin muffin recipe based on your dietary needs while keeping it as delicious as ever!
Are These Gluten Free Pumpkin Muffins Healthy?
When it comes to healthy pumpkin muffins, these are a fantastic choice. Not only do they satisfy your seasonal cravings, but they’re also packed with beneficial ingredients that make them a wholesome treat for almost any diet. Here’s why:
High in Protein
Each muffin contains 7 grams of protein, thanks to the addition of unflavored collagen peptides and eggs. This makes them a great choice for those looking to keep their energy levels up, whether it’s for breakfast or as a post-workout snack.
Naturally Dairy-Free & Gluten-Free
These muffins are free from dairy and gluten, making them suitable for people with lactose intolerance, celiac disease, or those following a gluten-free lifestyle. They’re also free from refined sugar, as they’re sweetened with coconut sugar, which has a lower glycemic index compared to regular sugar.
Packed with Nutrients
The key ingredient pumpkin puree is not only flavorful but loaded with nutrients like vitamin A, fiber, and antioxidants. This makes your muffins not only a delicious treat but also a way to support your immune system and promote healthy digestion.
Balanced in Fat & Carbs
With a combination of healthy fats from avocado oil and coconut sugar, and the carbohydrates from the gluten-free flour, these muffins provide a balanced energy source, helping to keep blood sugar levels stable without the crash that often comes from overly sweet treats.
No Added Preservatives
Unlike store-bought muffins, which are often loaded with preservatives, artificial flavors, and unhealthy fats, these healthy pumpkin muffins are made from simple, whole-food ingredients you can trust.
So, yes, these gluten free pumpkin muffins are not only tasty but also a much healthier alternative to traditional fall baked goods. They offer a perfect combination of protein, fiber, and healthy fats to keep you feeling satisfied and nourished.

How to Store and Freeze Your Pumpkin Muffins
These gluten free pumpkin muffins are incredibly moist and stay fresh for days, making them perfect for meal prep or enjoying throughout the week. Here’s how to store them and keep them at their best:
Storing at Room Temperature:
- Cool the Muffins: After baking, allow the muffins to cool completely in the muffin tin for about 10 minutes, then transfer them to a wire rack to cool completely.
- Airtight Container: Once cooled, place the muffins in an airtight container at room temperature. They should stay fresh for up to 4 days. If you live in a humid environment, consider placing a paper towel at the bottom of the container to absorb excess moisture and keep the muffins from getting soggy.
Freezing for Long-Term Storage:
- Flash-Freezing: If you’d like to store your muffins for longer, flash-freezing is the best option. Simply place the muffins on a tray in a single layer and freeze for 2 hours.
- Freezer Storage: Once frozen, transfer the muffins to an airtight freezer-safe bag or container. Label with the date and store for up to 3 months.
- Reheating: When you’re ready to enjoy, thaw the muffins overnight in the fridge or microwave them for 30–60 seconds until warmed through. You can also place them in a 350°F (175°C) oven for about 10 minutes to freshen them up.
By following these simple storage methods, you can enjoy these healthy pumpkin muffins whenever the craving strikes no matter the season!
More Gluten-Free Recipes To Try!

Gluten Free Pumpkin Muffins
Ingredients
Dry Ingredients:
- 1 ¼ cups gluten free 1-to-1 flour for the ideal texture without the gluten
- ½ cup unflavored collagen peptides adds protein without affecting taste or texture
- 1 tbsp pumpkin pie spice for that classic fall flavor
- 1 tsp baking powder for the perfect rise
- ¼ tsp baking soda works with the pumpkin puree to give the muffins the right fluff
- ½ tsp kosher salt enhances all the flavors
Wet Ingredients:
- 1 can 15 oz pumpkin puree (the star ingredient that keeps the muffins moist)
- 2 large eggs adds structure and protein
- ½ cup coconut sugar a healthier, lightly sweet alternative to refined sugar
- ¼ cup avocado oil or melted refined coconut oil for a neutral flavor
- 1 tsp vanilla extract for a touch of sweetness and depth
Mix-Ins:
- 1 cup paleo chocolate chips adds a rich, melty sweetness without dairy or refined sugar
Instructions
- Preheat your oven and prepare your muffin tin:
- Preheat the oven to 375°F (190°C). Line a muffin tin with paper liners or grease the tin to ensure easy removal once baked.
- Mix the dry ingredients:
- In a large bowl, whisk together the gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt. Ensure everything is well-combined for an even texture.
- Combine the wet ingredients:
- In another bowl, whisk together the pumpkin puree, eggs, coconut sugar, avocado oil, and vanilla extract until smooth. Make sure there are no lumps from the pumpkin puree.
- Add the dry ingredients to the wet ingredients:
- Gradually pour the dry ingredients into the wet mixture, stirring gently with a spatula. Mix until the batter is mostly combined but don’t overwork it — a few lumps are okay.
- Fold in the chocolate chips:
- Gently fold in the paleo chocolate chips using a spatula, ensuring they are evenly distributed throughout the batter.
- Rest the batter:
- Let the batter rest for 10–15 minutes. This step allows the flour to absorb the wet ingredients and helps the muffins rise better.
- Fill the muffin tin and bake:
- Divide the batter evenly among the 12 muffin cavities, filling each about 2/3 full. Bake for 22–25 minutes, or until a toothpick inserted into the center comes out clean with just a few moist crumbs attached.
- Cool and enjoy:
- Let the muffins cool in the tin for about 10 minutes, then transfer them to a wire rack to cool completely. Enjoy them fresh, or store for later!
Notes
Frequently Asked Questions About Pumpkin Muffin Recipes
Here are some common questions that often come up when making gluten free pumpkin muffins. Let’s address them to help ensure your baking success!
Can I use canned pumpkin pie filling instead of pumpkin puree?
No, it’s best to use pure pumpkin puree, not pumpkin pie filling. The filling contains added sugar and spices, which will affect the flavor and texture of your muffins. Stick with the plain puree for the best results.
Can I make these muffins without eggs?
Yes! If you need an egg-free version, you can substitute the eggs with flax eggs. To make a flax egg, combine 1 tablespoon of ground flaxseed with 2.5 tablespoons of water. Let it sit for a few minutes to thicken before adding it to the batter.
Can I make these muffins ahead of time?
Absolutely! These muffins stay fresh for up to 4 days at room temperature in an airtight container. For longer storage, you can freeze them for up to 3 months. Just make sure they’re fully cooled before freezing.
Can I use almond flour instead of gluten free flour?
Unfortunately, almond flour doesn’t work as a direct substitute for gluten free 1-to-1 flour in this recipe. If you’re looking for a grain-free option, you may need to adjust the recipe and measurements. If you’d like a fully grain-free muffin, consider a recipe specifically designed for almond flour.
How can I make these muffins sweeter?
If you prefer a sweeter muffin, feel free to add a little more coconut sugar or try a liquid sweetener like maple syrup. Just remember that adding extra liquid may require a slight adjustment in the dry ingredients to maintain the proper batter consistency.
These FAQs will help you troubleshoot common issues and ensure your healthy pumpkin muffins turn out perfectly!
Conclusion: Why These Gluten Free Pumpkin Muffins Are a Must-Try
These gluten free pumpkin muffins are the ultimate fall treat — moist, fluffy, and packed with nutrients. Whether you’re looking for a healthy pumpkin muffin recipe to enjoy on chilly mornings or a nutritious snack to satisfy your sweet tooth, this recipe ticks all the boxes. With paleo chocolate chips, collagen peptides, and the natural sweetness of coconut sugar, they offer a deliciously guilt-free way to indulge in the flavors of the season.
Not only do they provide a healthy dose of protein and fiber, but they’re also naturally dairy-free, making them suitable for a variety of dietary needs. Plus, with their moist texture and fluffy crumb, they’re sure to become a staple in your fall baking repertoire.
So, whether you’re meal prepping, baking for a special occasion, or just craving something sweet and cozy, these pumpkin muffins are a perfect fit. Give this recipe a try and experience just how easy it is to make a healthy, seasonal treat that everyone can enjoy!







