Gluten Free Pumpkin Muffins (High Protein)

These Gluten Free Pumpkin Muffins are a classic fall baked good made healthy! This recipe uses a whole can of pumpkin, is lightly sweetened with coconut sugar and packs in 7g of protein per muffin. They are super easy to make and hit the spot when you’re craving a healthy, festive treat!

Ahhh sweet September! It’s still a little early for Fall recipes, but I just don’t care anymore…gimme all the pumpkin and apple! Obviously one of my first festive fall recipes of the season has to be pumpkin muffins. They’re a classic for good reason.

I actually developed these gluten free pumpkin muffins last year after many requests from my husband. He’s a fiend for some pumpkin muffins (rightfully so). I was kinda unsatisfied with all the other pumpkin muffin recipes I was seeing online...many of them were loaded with tons of sugar, used a meager amount of pumpkin, etc.

I knew I had to take matters into my own hands, so I created the most perfect gluten free pumpkin muffin recipe that you’re staring at right now. Well obviously I’m bias, but I think it’s perfect for several reasons. 1) They’re gluten free, dairy free and refined sugar free, 2) they’re high in protein, 3) they’re made with healthy, wholesome ingredients and 4) they use a whole can of pumpkin!

And obviously they taste freaking incredible and are sooo moist too. Each of these healthy pumpkin muffins is studded with chocolate chips for the perfect balance of cozy spices and rich, melty chocolate. I’m almost positive they’re going to be meal prepped weekly throughout the duration of Fall, and I’m not even mad about it. The perfect healthy yet delicious treat!

Why You’ll Love these Gluten Free Pumpkin Muffins

• They are made with just a handful of simple, healthy ingredients!
• These gluten free pumpkin muffins use a whole can of pumpkin puree.
• They are lightly sweetened with coconut sugar.
• Each of these pumpkin muffins has 7g of protein!
• They’re gluten free, dairy free and refined sugar free.
• These are the perfect healthy fall baked good!

What You Need to Make these Protein Pumpkin Muffins

For the Dry Ingredients:

• Gluten Free 1-to-1 Flour: My favorite brands are Bob’s Red Mill and King Arthur Flour. Both of these contain xanthan gum which is a crucial ingredient! If you’re not gluten free, you can use an equal amount of normal AP flour.
• Unflavored Collagen Peptides: This is an easy way to add protein without affecting the taste or texture of the pumpkin muffins. If you don’t have this on hand or are vegetarian, simply swap in more gluten free 1-to-1 flour.
• Baking Powder: This recipe only has a mild amount of acidic ingredients, so it’s important to use predominantly baking powder as this leavening agent already has an acid.
• Baking Soda: Baking soda, on the other hand, needs an acid to react with.
• Pumpkin Pie Spice & Kosher Salt: Use a store-bought pumpkin pie spice blend for convenience and don’t forget that salt belongs in baked goods too!

For the Wet Ingredients:

• Pumpkin Puree: I love that this recipe uses an entire can of pumpkin puree so you don’t have annoying leftovers. Be sure to use pure pumpkin, NOT pumpkin pie filling.
• Eggs: 2 large eggs…I always use pasture-raised.
• Coconut Sugar: These gluten free pumpkin muffins are just lightly sweetened with coconut sugar, making them refined sugar free!
• Avocado Oil: Feel free to use this or any other neutral-flavored oil such as melted refined coconut oil.
• Vanilla Extract: Obvi! I recently bought this big jug of it on Amazon for super cheap.

For the Mix-ins:

• Paleo Chocolate Chips: To keep these pumpkin muffins gluten, dairy and refined sugar free, be sure to use some paleo chocolate chips. My favorite brand is Hu, and my discount code MADDIE will get you 20% off their whole website.

How To Make these Gluten Free Pumpkin Muffins

Preheat Oven & Prepare Muffin Tin:

First, preheat your oven to 375F and add liners to your muffin tin. Sometimes I like to be extra cautious and spray the inside of the liners with cooking spray…don’t wanna run the risk of muffin stickage!

Mix Together the Dry Ingredients:

Then, in a large bowl, whisk together the dry ingredients (gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda & kosher salt) until combined.

Mix together the Wet Ingredients:

Next, add all of the wet ingredients (pumpkin puree, eggs, coconut sugar, avocado oil & vanilla) to another large bowl. Whisk until combined and smooth.

Pour Dry Ingredients into Wet Ingredients:

Then, add dry ingredients to the wet ingredients and stir with a spatula until some flour is still visible.

Stir in Chocolate Chips:

Next, add in the chocolate chips and continue stirring until no more flour is visible, but do not over-stir! If you over-stir, the pumpkin muffins are more likely to turn out dense and dry. Less is more here.

Allow the batter to rest for 15 minutes. This will help the flour absorb the liquid ingredients and the baking powder will get working, leaving you with taller, fluffier muffins.

Pour into Muffin Tin & Bake:

Finally, divide batter evenly between the 12 muffin cavities. Top with a few extra chocolate chips, if desired. Transfer to the oven and bake for 22-25 minutes. Allow to cool for about 15 minutes in the pan, before transferring to a wire rack to finish cooling. Enjoy!

Are these Gluten Free Pumpkin Muffins Healthy?

Health is always subjective, but to me these gluten free pumpkin muffins fit the criteria for a healthy treat! They are just lightly sweetened with coconut sugar, so you won’t feel like you’re in a sugar coma after eating one.

I also love that these healthy pumpkin muffins have a good dose of protein (from the collagen and the eggs) and fats which is optimal for blood sugar balance. And of course…they’re gluten free, dairy free and refined sugar free so everyone can enjoy them!

Can I Omit or Substitute the Collagen?

As you’ll see in the full recipe card below, unflavored collagen peptides are one of the main dry ingredients in these healthy pumpkin muffins. Collagen, specifically this one from Vital Proteins, is a part of my daily routine – I love to sneak it in wherever I can! It not only dissolves into anything, but it also doesn’t impact the flavor. Plus, it’s a great source of clean protein and has many hair, skin and nail benefits.

However, if you don’t have any collagen on hand or want to make these pumpkin muffins vegetarian, you can substitute more gluten free 1-to-1 flour. In other words, omit the collagen and instead increase the flour to 1.75 cups (218g).

Can I Substitute Almond Flour or Coconut Flour?

No, sorry! Unfortunately, almond flour and coconut flour perform VERY differently than gluten free 1-to-1 flour so they are not interchangeable. I would pretty much have to develop a whole new recipe with different measurements. If you’re interested in a grain-free pumpkin muffin recipe, I can definitely prioritize developing one!

Expert Tips & Tricks:

These gluten free pumpkin muffins are quite simple to make, but these tips and tricks will help ensure they turn out perfect!

• Use a kitchen scale to measure the ingredients: For the most accurate results, use a kitchen scale (they’re super cheap on amazon) to measure the ingredients, especially the dry ones. If you don’t own one, make sure to measure the flour with the spoon and level method.
• Do not over-mix the batter: You’ll want to add the chocolate chips in while there is still plenty of flour visible in the batter. Then, mix until just combined so that the muffins don’t become dry or dense.
• Use a toothpick or chopstick to test muffin doneness: After 22 minutes of baking, poke a hole in the center of a muffin. The muffins are done if they come out mostly clean with a few moist crumbs. Remember…they’re going to continue cooking a bit as they cool.

Can I Freeze these Healthy Pumpkin Muffins?

Yes! First, allow these healthy pumpkin muffins to cool down completely. Then, transfer them to a tray or plate and pop them in the freezer for about 2 hours to “flash freeze.” After that, move them over to an airtight container or a freezer bag.

When you’re ready to re-heat these pumpkin muffins, you can either thaw them in the fridge overnight or for a quicker option, microwave them for 30-60 seconds or until warmed through.

How Should I Store these Gluten Free Pumpkin Muffins?

Leftover gluten free pumpkin muffins should be cooled fully before transferring to an airtight container and storing them at room temperature for about 4 days…if they last that long 😉 Luckily, these muffins stay super moist but you can always microwave them for 15-30 seconds if you want the chocolate chips to get gooey!

Find the full recipe below. As always, please let me know if you tried it by commenting below or tagging me on Instagram, @munchinwithmaddie_.

Looking for More Healthy Dessert Recipes?

• Paleo Brownies with Sweet Potato and Tahini
• Gluten Free & Dairy Free Carrot Cake Muffins
• Paleo Almond Orange Loaf Cake
• Gluten Free Monster Cookies
• Red Velvet Muffins (No Food Dye!)
• Paleo Apple Crisp for Two
• Gluten Free Lemon Poppyseed Muffins

5 from 12 votes

Gluten Free Pumpkin Muffins (High Protein)

These Gluten Free Pumpkin Muffins are a classic fall baked good made healthy! This recipe uses a whole can of pumpkin, is lightly sweetened with coconut sugar and packs in 7g of protein per muffin. They are super easy to make and hit the spot when you're craving a healthy, festive treat!

Servings 12 muffins

Prep Time 10 minutes mins

Cook Time 25 minutes mins

Resting Time 15 minutes mins

Total Time 50 minutes mins

Equipment

• 2 large bowls
• whisk
• spatula
• muffin tin with liners

Ingredients

For the Dry Ingredients:

• 1 ¼ cup gluten free 1-to-1 flour (156g)*
• ½ cup unflavored collagen peptides (49g)**
• 1 tbsp pumpkin pie spice
• 1 tsp baking powder
• ¼ tsp baking soda
• ½ tsp kosher salt

For the Wet Ingredients:

• 1 can pumpkin puree (15oz)
• 2 large eggs
• ½ cup coconut sugar (81g)
• ¼ cup avocado oil or melted refined coconut oil
• 1 tsp vanilla extract

For the Mix-Ins:

• 1 cup paleo chocolate chips (182g)

Instructions

• Preheat your oven to 375F and add liners to your muffin tin.
• In a large bowl, whisk together the dry ingredients until combined.
  1 ¼ cup gluten free 1-to-1 flour, ½ cup unflavored collagen peptides, 1 tbsp pumpkin pie spice, ¼ tsp baking soda, ½ tsp kosher salt, 1 tsp baking powder
• In another large bowl, whisk together all of the wet ingredients until smooth. Then, add dry ingredients to the wet ingredients and stir with a spatula until some flour is still visible.
  1 can pumpkin puree, 2 large eggs, ½ cup coconut sugar, ¼ cup avocado oil, 1 tsp vanilla extract
• Add in the chocolate chips and continue stirring until no more flour is visible, but do not over-stir! Allow the batter to rest for 15 minutes.
  1 cup paleo chocolate chips
• Divide batter evenly between the 12 muffin cavities. Top with a few extra chocolate chips, if desired. Transfer to the oven and bake for 22-25 minutes. The muffins will be quite moist, so it's important to let them cool down for a bit before eating. Allow them to cool in the muffin tin for 15 minutes, before transferring to a wire rack to finish cooling. Enjoy!

Video

Notes

GENERAL NOTE: For the most accurate results, use a digital kitchen scale to measure your ingredients. If you don’t own one, be sure to measure the flour with the spoon and level method.

*NOTE: My two favorite brands are Bob’s Red Mill and King Arthur Flour, both of which contain xanthan gum – a crucial ingredient to replicate gluten-filled baked goods. If you’re not gluten free, you can substitute an equal amount of normal AP flour.

**NOTE: If you don’t have any collagen on hand or want to make these muffins vegetarian-friendly, just omit the collagen and increase the amount of gluten free 1-to-1 flour to 1.75 cups (218g). 

NUTRITION INFO REVISION (10/7/24): The nutrition facts had originally stated that each muffin has 13g of protein, however it has since been revised down to 7g of protein per muffin. The plug-in that helps me calculate the macros was pulling inaccurate data for the collagen – apologies for the inconvenience!

Calories: 216kcal

Course: Dessert, Snack

Cuisine: American

Diet: Gluten Free, Dairy Free

Keyword: Baked Goods, Chocolate Chips, Dairy Free, Fall Recipe, Gluten Free, Healthy Dessert, High Protein, Muffin, Pumpkin, Pumpkin Spice, Refined Sugar Free

Nutrition

Calories: 216kcal | Carbohydrates: 27g | Protein: 7g | Fat: 11g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Trans Fat: 0.003g | Cholesterol: 27mg | Sodium: 199mg | Potassium: 87mg | Fiber: 3g | Sugar: 13g | Vitamin A: 5553IU | Vitamin C: 2mg | Calcium: 64mg | Iron: 2mg

Did you make this recipe?

Please let me know how it turned out for you! Leave a comment below and tag @munchinwithmaddie_ on Instagram and/or hashtag it #munchinwithmaddie.