Paleo Pumpkin Protein Muffins: Easy, Nutritious, and Gluten-Free!
These Paleo Pumpkin Protein Muffins are quick and easy snacks, lunch boxes, or breakfast items. They’re effortless to make, healthy, gluten-free, dairy-free, and even have a nut-free option. Whether you’re cozying up for fall or need a protein-packed snack to power through your day, these muffins are the answer.
Why You’ll Love These Muffins
These muffins are a dream for anyone seeking high-protein snacks. They’re made with wholesome ingredients like almond flour, collagen, and pure canned pumpkin, providing a perfect blend of flavor and nutrition. Not only are they gluten-free and dairy-free, but they also fit seamlessly into a Paleo diet. And the best part? They come together in under 30 minutes, making them an easy addition to your weekly meal prep.
Ingredients You’ll Need
- Almond Flour: The base of these muffins, offering a light and tender crumb. If you need a nut-free option, you can easily swap this for cassava flour instead. See recipe notes for details. I prefer “super-fine” almond flour to get the best texture. I like this one from Blue Diamond I can get at Sam’s Club or Amazon.
- Tapioca Flour: Adds a bit of elasticity and helps bind the muffins together, giving them that perfect muffin texture without any gluten. Though you can use arrowroot or potato starch instead, tapioca is ideal for it’s ability to give a stretch to baked Paleo good that can be dry. Learn more about Paleo flours and how to use them here.
- Collagen Peptides: The secret ingredient that boosts the protein content, making these muffins not just tasty but also a great source of protein. Yes, you can use another unflavored protein powder of your choice in these as well. There are a lot of collagen brands out there. Use what is most accessible to you. I often get Vital Proteins unflavored collagen when it is on sale at Costco. I love and use regularly BUBS Collagen, which is Whole30 Approved.
- Baking Powder and Salt: Essential for a good rise and to balance the flavors.
- Canned Pumpkin: Make sure it’s pure pumpkin, not the pie filling. This ingredient not only adds moisture but also a wonderful autumn flavor.
- Maple Syrup: A natural sweetener that complements the pumpkin perfectly and keeps these muffins refined sugar-free.
- Extra Light Tasting Olive Oil or Avocado Oil: Either of these oils will work well, providing moisture without overpowering the delicate flavors. I usually use extra light-tasting olive oil due to cost. But, make sure it’s “extra light tasting,” not regular olive oil.
- Eggs: They help bind the ingredients together and give the muffins their structure. I do not have a egg-free variation for these muffins. BUT, please leave a comment below if you find one that works well for you, to help others!
- Pumpkin Pie Spice: Because what’s a pumpkin muffin without a warm blend of spices? This adds that cozy, comforting flavor that makes these muffins irresistible. Can’t find a pumpkin pie spice at your store? Make your own with an easy recipe like this one.

Instructions
- Preheat your oven to 350°F (175°C). Prepare a muffin tin with parchment paper liners or a light coating of olive or avocado oil.
- Mix the dry ingredients: In a large bowl, combine the almond flour, tapioca flour, collagen peptides, baking powder, salt, and pumpkin pie spice. Stir until well combined, ensuring there are no clumps.
- Prepare the wet ingredients: In a separate bowl, whisk together the canned pumpkin, maple syrup, olive oil (or avocado oil), and eggs. Make sure the mixture is smooth and well combined.
- Combine the mixtures: Gradually add the wet ingredients to the dry ingredients, stirring just until everything is combined. Be careful not to overmix; you want the muffins to be light and fluffy.
- Fill the muffin tin: Divide the batter evenly among the prepared muffin cups, filling each ALL the way full. These won’t rise as much as regular muffins with gluten.
- Bake: Place the muffin tin in the preheated oven and bake for 30 minutes. They are done when you touch the top of the muffins and they bounce back.
- Cool and enjoy: Let the muffins cool in the tin for a few minutes before transferring them to a wire rack to cool completely. These muffins are delicious warm, but they also store well for later.
Nut-Free Option
If you or someone in your family needs a nut-free option, simply substitute the almond flour with cassava flour. This easy swap making these muffins safe for nut-free diets. See recipe notes for exact amounts and details.
Why These Muffins Are Perfect for You
These Paleo Pumpkin Protein Muffins are more than just a tasty treat. They’re packed with protein from the collagen peptides, making them ideal for a post-workout snack or a quick breakfast. The combination of almond and tapioca flours gives them a soft, tender crumb that’s entirely gluten-free, while the pumpkin offers a boost of fiber and essential nutrients.
With natural sweetness from maple syrup and the warm spices of pumpkin pie spice, these muffins are a delightful, guilt-free indulgence. And since they’re dairy-free, they’re a perfect fit for anyone with lactose intolerance or those following a strict Paleo diet.

Protein-Packed and Paleo-Approved
These Pumpkin Protein Muffins are a great way to incorporate more protein into your diet while sticking to your Paleo lifestyle. They’re not only delicious and easy to make but also packed with wholesome, nutritious ingredients that will keep you satisfied and energized throughout the day. Whether you enjoy them as a quick breakfast, a healthy protein snack, or a cozy fall treat, these muffins are sure to become a favorite in your kitchen.
With search-friendly keywords like “Protein Muffins Gluten Free” and “Pumpkin Protein Muffins,” these muffins are not just a great snack but also a recipe that’s easy to find and share. Get ready to enjoy a batch of these Paleo-approved, protein-packed muffins that are sure to become a staple in your home!
Other Paleo Muffins you might love:

Paleo Pumpkin Protein Muffins
Ingredients
- 3 cups almond flour (see notes for nut-free)
- 1/2 cup tapioca flour
- 1/2 cup unflavored collagen powder or protein powder* see note
- 2 teaspoons baking powder
- 2 teaspoons pumpkin pie spice
- 1/4 teaspoon salt
- 1 1/2 cups canned pureed pumpkin
- 1/2 cup maple syrup
- 1/4 cup light tasting olive oil or avocado oil, can sub melted coconut oil
- 2 large eggs
Instructions
- Preheat your oven to 350°F (175°C). Prepare a muffin tin with parchment paper liners or a light coating of olive or avocado oil.
- Mix the dry ingredients: In a large bowl, combine the almond flour, tapioca flour, collagen peptides, baking powder, salt, and pumpkin pie spice. Stir until well combined, ensuring there are no clumps.
- Prepare the wet ingredients: In a separate bowl, whisk together the canned pumpkin, maple syrup, olive oil (or avocado oil), and eggs. Make sure the mixture is smooth and well combined.
- Combine the mixtures: Gradually add the wet ingredients to the dry ingredients, stirring just until everything is combined. Fold in chocolate chips, if using.
- Fill the muffin tin: Divide the batter evenly among the 12 prepared muffin cups, filling each ALL the way full. Yes, all the way full, not just 3/4th full for these muffins.
- Bake: Place the muffin tin in the preheated oven and bake for 30 minutes. They are done when you touch the top of the muffins and they bounce back.
- Cool and enjoy: Let the muffins cool in the tin for a few minutes before transferring them to a wire rack to cool completely. These muffins are delicious warm, but they also store well for later.
- To Freeze: Freeze in a single layer. Once frozen, store in a sealed container for up to 3 months.
















I make these almost every week! Love them so much! How do you store them? I typically put them in a container on the counter but noticed there is a lot of moisture building. Is the fridge better?
So glad you love them!! Yes — I recommend storing them in the fridge once they’ve fully cooled, or on the counter only covered with a towel. They do get a weird “wet” top if you store them sealed on the counter. If putting into the fridge, leave the lid slightly ajar until they cool completely, then store airtight in the fridge for best texture!
These were delicious! Thank you for yet another great recipe!
So glad you enjoyed them! 🎉 Thank you for making them and for the kind feedback — it means a lot!
This recipe is fantastic! I’m shocked that it has such a great texture. Healthy, delicious and protein packed- a huge win!
So glad you loved it! 🙌 I’m thrilled to hear the texture and flavor hit the mark—healthy, delicious, and protein-packed really is the best combo. Thanks for the awesome review!
Just made these for the first time.. delicious! Wondering if they freeze ok?
delicious and I love that they have protein in them! Wondering if they freeze ok?
Yes, they freeze great! Just freeze them in a single layer first, then transfer to a sealed bag or container so they don’t stick together. Thanks so much for asking!
Great texture! I added crumb to the top on one occasion and I highly recommend. Kids and adults alike enjoyed them!
So happy that everyone—kids and adults—enjoyed them! And that crumb topping is such a yummy upgrade. Thanks so much for taking the time to leave a review!
Love them! So does my 9 year old!
Woohoo, thank you! I’m so happy it was enjoyed, and kid wins are the best. Thanks much for the review – those help me a ton!
I’e been making the banana version of these for awhile now, and made the pumpkin ones this weekend. I have 4 kids ages 4-11 and they ALL like them which is passing a huge test for a recipe. They feel like they’re getting a treat and I know they’re healthy. Feels like a big mom flex! (& I like them too!)
What a joy to hear! YAAAY that they passed the toughest taste-testers,kid-wins are the best. Thank you for your review, and I’m so happy it was a hit!
Currently obsessed with these. The second time I made them I added two scoops of unflavored whey protein for even more of a protein boost. It worked really well.
Yes! So glad you love these, and it was one you wanted to make again. Thanks for sharing what modifications you used and enjoyed. I appreciate the review—thank you!
Your recipe was perfect timing. Was looking for a new fun protein packed breakfast/snack option and these were delicious! Didn’t add the chocolate chips, and literally needs nothing extra. But, I couldn’t resist putting just a touch of peanut butter on top. Highly recommended! These will be in rotation throughout Fall!
So great to hear this was a success! We have been loving these all fall. Thanks for letting me know, and for the awesome review!
These are unbelievable. The texture is out of this world and the flavor is absolutely amazing. All with the added bonus of some sneaky protein. Like… so, SO good. Thank you for sharing this with us!
“Unbelievable” texture?! WAHOO! I’m so glad you found these just spot on both texture and flavor. Thank you so much for the rave review!
Delicious! I wanted to try these so bad but was out of almond flour. I used the nut free cassava and the muffins were good. Then I made them with almond flour. Oh my goodness! Amazing! Instead of chocolate chips, I added pecans.
So happy to hear you enjoyed it! I agree, I love the almond flour version best – it adds extra moisture and richness. So glad you found them amazing! Thanks a ton for the feedback!
Do these freeze ok?
Yes, they freeze great! Just freeze them in a single layer first, then transfer to a sealed bag or container so they don’t stick together. Thanks so much for asking!
Another protein muffin hit! Because I wanted to take a deep dive into the fall flavors, I added 1/2 c chopped pecans and 2 tablespoons of chopped, candied ginger to the mix.
I’m so happy you loved these! And thanks for letting me know what add-ins you enjoyed, I love hearing that. Thanks so much for the review!
Can I substitute for oat flour?
That’s a great question. As these are Paleo and grain-free, I haven’t tested any oat or 1:1 gluten-free flour. I’m sure it could work, it would just take some tinkering to get the right amount. Let me know if you try it and how it works out!
I made this without the chocolate chips and added Autumn’s glaze from her doughnuts recipe in her cookbook and it was so yummy! I think it would be good with a cream cheese frosting too! Love that there is protein in these too! Ready for fall!
Great call on the glaze or cream cheese frosting, I will have to add that option in. I’m glad they are a new fall favorite! Thank you!
So yummy! Perfect for chilly fall mornings with my coffee.
Hooray! I’m so glad you made and love this fall muffin. Delicious and easy. Thank you for the review!