Best Pumpkin Muffins Recipe (Gluten Free + High Protein)
Updated: November 6, 2025
If there’s one thing I get excited about every fall, it’s pumpkin recipes. I love a good pumpkin bread or pumpkin spice latte, but this high-protein and gluten-free pumpkin muffins recipe might just be my all-time favorite way to enjoy pumpkin. They’re just sweet enough, super soft and fluffy, and made with wholesome ingredients I almost always have on hand. Plus, they’re dairy-free, refined- sugar free, and come together in one bowl.
These muffins have quickly become one of my go-to staples. It’s an easy way to sneak in a little extra protein while enjoying a cozy sweet treat. Whether I’m prepping breakfasts for the week or just want something comforting to go with my coffee, they always hit the spot.
Want More Pumpkin Recipes? Try my: Pumpkin Spice Whipped Cream, Pumpkin Spice Cold Foam, Pumpkin Cheesecake Truffles, Pumpkin Cheesecake Dip, Roasted Pumpkin Seeds in the Air Fryer + Pumpkin Spice Chai Latte!
Why You’ll Love This Pumpkin Muffin Recipe
As a Nutritional Therapist Practitioner (NTP) and former chef to professional athletes, I'm obsessed with creating treats that are both delicious and genuinely good for you. These muffins earned a permanent spot in my fall rotation because they hit all the important notes:
Built for Performance and Health: They pack in protein to keep you feeling full, a key factor I considered when designing meal plans for top athletes.
Naturally Fueling: Sweetened perfectly with maple syrup and utilize almond flour, making them gluten-free, refined-sugar-free, refined-flour-free, and dairy-free.
One-Bowl Ease: Made in one large bowl so cleanup is minimal, perfect for busy weeknight meal prep.
Family-Approved & Freezer-Ready: Whether you’re prepping breakfasts for the week or looking for a higher protein snack that the kids (and adults) will love, these muffins check all the boxes!
Check Out My New Cookbook!
My Favorite Protein Powder
I used FlavCity Vanilla Cream protein powder for these muffins because it’s honestly my favorite vanilla protein. It’s super smooth and not chalky like a lot of protein powders. I find that it mixes in perfectly with baked goods. I also love the ingredients: it’s made with clean, simple ingredients (no weird artificial stuff), so I feel good about giving it to my family.
What About the Chocolate Chips?
I love using Enjoy Life mini chocolate chips in baking because they’re dairy-free, allergy-friendly, and made with really simple ingredients. just pure chocolate without anything funky added, so I feel good about using them in recipes for kids and adults.
Which Canned Pumpkin Should I Use?
Use a canned pumpkin that is 100% pure pumpkin. Make sure it’s not pumpkin pie filling, which is made with tons of sugars, and added ingredients.
How to Make These Kid-Friendly!
Skip the chocolate chips if you want less sugar, or use mini chips so you can add just a little bit.
Ingredients You’ll Need
Here’s what you’ll need to make these healthy pumpkin protein muffins. You should be able to find everything at your local grocery store!
1 cup canned pumpkin (make sure it’s 100% pure pumpkin, not pumpkin pie filling)
2 large eggs (room temp is best)
1/4 cup maple syrup (or honey if that’s what you’ve got)
1 1/2 cups almond flour
1/2 cup vanilla protein powder (I used FlavCity Vanilla Cream)
1 teaspoon baking powder
1 1/2 teaspoons pumpkin pie spice
1/4 cup mini chocolate chips + more for topping (I love Enjoy Life mini chips!)
1 teaspoon vanilla extract
Jazz's Recommended Products
Glass Mixing Bowls – Great for mixing your wet and dry ingredients.
FlavCity Vanilla Protein Powder – My go-to for boosting the protein content in muffins and other baked goods.
Small Whisk – Perfect for whisking together wet ingredients.
Nonstick Muffin Tin – A must-have for evenly baked muffins every time.
Enjoy Life Mini Chocolate Chips – Dairy-free and allergy-friendly, ideal for kid-friendly treats.
How To Make My High-Protein Pumpkin Muffins
You’ll need a large mixing bowl, a small whisk, and a rubber spatula. Also, grab your muffin tin (or muffin pan) and line it with paper liners.
1. Preheat the oven to 350°F and line a muffin tin with paper liners.
2. In a large bowl, whisk together pumpkin, eggs, maple syrup, and vanilla.
3. Add almond flour, protein powder, baking powder, and pumpkin pie spice. Stir until just combined. Careful not to over-mix.
4. Fold in chocolate chips gently.
5. Scoop batter into muffin cups, filling each about 3/4 full. Smooth out the tops with a spoon, and sprinkle a few more chocolate chips on top of each one (these will look so good once baked).
6. Bake for 18–20 minutes or until a toothpick inserted into the center comes out clean.
7. Let muffins cool for at least 10 minutes before removing from the tin.
Want More Sweet Treats?
If you love these pumpkin muffins, you might also enjoy some of my other favorite recipes:
Serving Ideas
These muffins are perfect for breakfast-on-the-go, a lunchbox snack, or a cozy afternoon pick-me-up. Spread a little nut butter on top for extra protein or enjoy with a smoothie for a quick, balanced meal. They also make a great after-school snack for kids!
They also taste amazing with a cup of tea or coffee on a cozy afternoon.
Storage Tips
To keep these muffins fresh and delicious:
Let them cool fully before storing—this helps prevent sogginess.
Store in an airtight container at room temperature for up to 2 days.
For longer freshness, refrigerate for up to 5 days.
Want to make them last even longer? Freeze in a single layer inside a freezer bag.
Ingredient Swaps & Substitutions
Nut-free: Use oat flour instead of almond flour.
No pumpkin pie spice? Use 1 tsp cinnamon + 1/4 tsp nutmeg + 1/4 tsp ginger.
Sweetener swap: Honey or agave works in place of maple syrup.
Boost the sweetness: Add an extra tablespoon of syrup or a few chocolate chips on top before baking.
Protein powder: Both plant-based and whey protein work. Pick a vanilla flavor you actually like.
Troubleshooting Tips
Grease muffin tins: make sure you grease the muffin liners if you are using any!
When Mixing: Don’t over-mix the batter just gently stir until combined.
Filling the muffins: Only fill muffin cups 3/4 full so they bake evenly and don’t spill over.
Muffins sunk in the middle: If they sink in the middle, they just needed a few extra minutes in the oven, check with a toothpick before pulling them out.
Muffins sticking to the pan: Let muffins cool for at least 10 minutes before removing, or use parchment muffin liners to avoid sticking.
Too wet/dense: Make sure you use the exact amount of pumpkin (1 cup) and don’t add extra liquid.
Make them last longer: Freeze muffins in a zip-top bag for up to 2 months. Thaw at room temperature or microwave for 20 seconds.
FAQs
-
Yes! Swap the almond flour for oat flour (same amount). The texture will be a little more dense but still tasty.
-
A vanilla protein powder you actually enjoy. Plant-based or whey both work, just avoid one that’s very gritty or overly sweet.
-
Yes, but they’ll be more dense. Use 2 flax eggs (2 tbsp ground flax + 5 tbsp water) and bake a few extra minutes.
-
Once cooled, store in an airtight container on the counter for up to 2 days or in the fridge for up to 5 days. They also freeze well for up to 2 months.
-
They’re lightly sweetened with maple syrup. For a sweeter muffin, add a tablespoon more syrup or extra chocolate chips on top.
-
Absolutely. They’re optional, but they make these muffins extra kid-friendly. You can swap for walnuts, pumpkin seeds or any other nuts!
These high protein pumpkin muffins have become a go-to in my kitchen, especially during this time of year. They’re cozy, satisfying, and made with better-for-you ingredients that actually taste good. If you’re on the hunt for healthy pumpkin muffins that boost your protein content or just want something pumpkin-y without the refined sugar and gluten, this easy recipe is one you’ll come back to again and again.
If you’re craving that cozy fall feeling, this might just be the best pumpkin muffin recipe to try. It’s packed with warm pumpkin flavor and comes together so easily that these easy pumpkin muffins have become one of my favorite muffin recipes. They’re soft, perfectly sweet, and honestly some of the best muffins to bake when you want something comforting. These really are the best pumpkin muffins for anyone who loves a true classic pumpkin muffin with rich pumpkin flavor.
Easy High Protein Pumpkin Muffins (Gluten Free)
These easy high-protein pumpkin muffins are soft, fluffy, and full of cozy fall flavor. Made in one bowl with wholesome ingredients like almond flour, canned pumpkin, and vanilla protein powder, they’re gluten-free, dairy-free, naturally sweetened, and free of refined sugar or flour. Kid-friendly, freezer-friendly, and perfect for breakfast, snacks, or meal prep.
Ingredients
- 1 cup canned pumpkin (make sure it’s 100% pure pumpkin, not pumpkin pie filling)
- 2 large eggs (room temp is best)
- 1/4 cup maple syrup (or honey if that’s what you’ve got)
- 1 1/2 cups almond flour
- 1/2 cup vanilla protein powder (I used FlavCity Vanilla Cream)
- 1 teaspoon baking powder
- 1 1/2 teaspoons pumpkin pie spice
- 1/4 cup mini chocolate chips + more for topping (I love Enjoy Life mini chips!)
- 1 teaspoon vanilla extract
Instructions
- Preheat the oven to 350°F and line a muffin tin with paper liners.
- In a large bowl, whisk together pumpkin, eggs, maple syrup, and vanilla.
- Add almond flour, protein powder, baking powder, and pumpkin pie spice. Stir until just combined. Careful not to over-mix.
- Fold in chocolate chips gently.
- Scoop batter into muffin cups, filling each about 3/4 full. Smooth out the tops with a spoon, and sprinkle a few more chocolate chips on top of each one (these will look so good once baked).
- Bake for 18–20 minutes or until a toothpick inserted into the center comes out clean.
- Let muffins cool for at least 10 minutes before removing from the tin.
This easy, high-protein pumpkin muffin recipe is soft, fluffy, and full of cozy fall flavor. Made with wholesome ingredients like almond flour, canned pumpkin, and vanilla protein powder, they’re gluten-free, dairy-free, and perfect for breakfast, snacks, or meal prep.