Soft Protein-Packed Pumpkin Muffins

Section: Quick Snacks & Appetizers

These gluten-free pumpkin muffins offer a tender, moist texture enriched with real pumpkin and warming pumpkin pie spice. Collagen peptides add a subtle protein boost, paired with paleo chocolate chips folded in gently for pockets of sweetness. The batter rests before baking to improve rise and crumb, resulting in light, soft muffins perfect for autumn snacking or meal prep. Mildly sweetened with coconut sugar and balanced with vanilla and coconut oil, they provide a cozy, wholesome flavor. Store airtight at room temperature or freeze for freshness.

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Last modified on Sat, 27 Dec 2025 13:56:39 GMT
A plate of muffins with chocolate chips. Pin it
A plate of muffins with chocolate chips. | dinabakery.com

These gluten free pumpkin muffins are soft, sweet, and packed with protein, making them a perfect snack or breakfast treat during the fall season. They combine real pumpkin, cozy spices, and paleo chocolate chips for an irresistible flavor that also fits well within paleo and gluten free diets.

I first baked these muffins on a crisp fall morning and was amazed by how moist and delicious they were. Since then, they have become my go-to recipe when I want something both indulgent and nourishing.

Ingredients

  • Gluten free 1-to-1 flour: with xanthan gum to ensure the muffins rise well and hold together without gluten
  • Unflavored collagen peptides: bring protein and softness. For a vegetarian option increase the flour instead
  • Pumpkin pie spice: for classic fall flavor with notes of cinnamon, nutmeg, and clove. Choose a blend that smells fresh for best results
  • Baking powder and baking soda: provide lift to keep the muffins light and fluffy
  • Kosher salt: balances sweetness and enhances flavor
  • Pumpkin puree: adds moisture, natural sweetness, and that signature fall taste. Use pure pumpkin, not pumpkin pie filling
  • Large eggs: bind ingredients and enrich the texture
  • Coconut sugar: gives a mild caramel-like sweetness while keeping the recipe paleo-friendly
  • Avocado oil or melted refined coconut oil: for richness without overpowering the pumpkin
  • Vanilla extract: rounds out the flavor profile with warmth and aroma
  • Paleo chocolate chips: add melty pockets of chocolate and are grain free. You can top muffins with them for a pretty finish

Step-by-Step Instructions

Preheat and Prepare:
Set your oven to 375 degrees Fahrenheit and line a muffin tin with paper liners. Lightly spray the liners if you like for easy removal. This upfront step ensures your muffins cook evenly and don’t stick.
Mix Dry Ingredients:
In a large bowl, whisk together the gluten free flour, collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt. This evenly distributes the leavening agents and spices, critical for a consistent rise and flavor.
Whisk Wet Ingredients:
In a separate bowl, combine the pumpkin puree, eggs, coconut sugar, oil, and vanilla extract. Whisk until the batter looks smooth and homogenous. This step helps avoid lumps and creates a tender crumb.
Combine Wet and Dry:
Pour the dry ingredients into the wet bowl and stir gently just until you still see some flour. Overmixing leads to tough muffins so a light touch is key here.
Fold in Chocolate Chips:
Add the paleo chocolate chips and fold carefully until the flour disappears. Do not overmix or you risk a dense muffin texture.
Rest the Batter:
Let the batter sit for 15 minutes. This resting period improves the muffins’ rise and texture by allowing the gluten free flour to fully hydrate.
Fill Muffin Liners and Add Toppings:
Divide the batter evenly between the 12 muffin liners. Sprinkle extra chocolate chips on top for a melted sweet surprise and an appealing look.
Bake and Cool:
Bake the muffins for 22 to 25 minutes until a toothpick inserted into the center comes out clean. Allow them to cool in the tin for 15 minutes before moving to a wire rack. This helps them firm up so they do not break apart.
Chocolate chip muffins with orange filling. Pin it
Chocolate chip muffins with orange filling. | dinabakery.com

My favorite ingredient has to be the pumpkin pie spice because it instantly evokes cozy fall memories. Baking these muffins with my kids has become a seasonal tradition we all look forward to as the weather cools.

Storage Tips

Keep these muffins in an airtight container at room temperature and they will stay fresh for up to four days. For longer storage, flash freeze them individually then transfer to a sealed container or freezer bag. Reheat for about 30 to 60 seconds in the microwave before eating for that fresh-baked feel.

Ingredient Substitutions

If you prefer a vegetarian version, simply replace the collagen peptides with additional gluten free flour, increasing the total flour amount to one and three-quarter cups. Avoid substituting almond or coconut flour here as they absorb liquid differently and change the muffin texture.

Serving Suggestions

A bowl of muffins with chocolate chips. Pin it
A bowl of muffins with chocolate chips. | dinabakery.com

These muffins are wonderful enjoyed plain or warm with a little butter or nut butter spread. Pair them with a cup of pumpkin spice latte or your favorite tea for a cozy autumn snack.

Frequently Asked Questions

→ What type of flour is best for these muffins?

Using a gluten-free 1-to-1 flour blend with xanthan gum is essential to achieve the right texture and rise.

→ Can I make these muffins vegetarian?

Yes, replace the collagen peptides with additional gluten-free flour to maintain the texture while keeping the muffins vegetarian.

→ How does letting the batter rest help?

Resting the batter for 15 minutes improves the muffins' rise and gives a tender crumb by allowing the flour to fully hydrate.

→ What sweetener is used in these muffins?

Coconut sugar provides a subtle sweetness that complements the pumpkin and spices without overpowering.

→ How should these muffins be stored for freshness?

Store them in an airtight container at room temperature for up to four days, or flash freeze for longer storage.

→ Why avoid almond or coconut flour substitutions?

Almond and coconut flours bake differently, affecting texture and moisture, so they aren't recommended for this particular mix.

Soft Protein-Packed Pumpkin Muffins

Soft, spiced gluten-free pumpkin muffins with protein and paleo chocolate chips for a cozy, wholesome treat.

Prep Time
10 minutes
Cooking Time
25 minutes
Total Preparation Time
35 minutes
By: Dina

Featured in: Snacks

Difficulty Level: Medium

Cuisine Type: American

Number of Portions: 12 Serving Size (12 muffins)

Dietary Options: Gluten-Free, Dairy-Free

The Ingredients You'll Need

→ Dry Ingredients

01 1¼ cups gluten free 1-to-1 flour blend with xanthan gum
02 ½ cup unflavored collagen peptides
03 1 tbsp pumpkin pie spice
04 1 tsp baking powder
05 ¼ tsp baking soda
06 ½ tsp kosher salt

→ Wet Ingredients

07 1 can (15 oz) pumpkin puree
08 2 large eggs
09 ½ cup coconut sugar
10 ¼ cup avocado oil or melted refined coconut oil
11 1 tsp vanilla extract

→ Add-ins

12 1 cup paleo chocolate chips, plus additional for topping

Step-by-Step Instructions

Step 01

Preheat the oven to 375°F and line a muffin tin with liners, lightly spraying them if desired.

Step 02

Whisk together the gluten free flour blend, collagen peptides, pumpkin pie spice, baking powder, baking soda, and kosher salt in a large mixing bowl.

Step 03

In a separate bowl, whisk together the pumpkin puree, eggs, coconut sugar, avocado or coconut oil, and vanilla extract until smooth.

Step 04

Add the dry ingredients to the wet ingredients and gently stir until some flour streaks remain visible.

Step 05

Carefully fold in the paleo chocolate chips just until the flour disappears; avoid overmixing to maintain a tender texture.

Step 06

Allow the batter to rest for 15 minutes to enhance rise and improve texture.

Step 07

Divide the batter evenly into 12 muffin liners and sprinkle with additional chocolate chips on top.

Step 08

Bake for 22 to 25 minutes until a toothpick inserted comes out clean. Let muffins cool in the pan for 15 minutes before transferring to a wire rack.

Extra Tips

  1. Use a kitchen scale for precise measurement. For a vegetarian option, replace collagen peptides with an extra ½ cup gluten free flour (total 1¾ cups). Avoid substituting almond or coconut flour as they affect the baking outcome. Store muffins in an airtight container at room temperature for up to 4 days or freeze after flash freezing, reheating 30–60 seconds before serving.

Tools You'll Need

  • Muffin tin
  • Mixing bowls
  • Whisk
  • Measuring cups and spoons
  • Wire cooling rack

Allergy Information

Check ingredient labels to avoid allergens, and speak to an expert if necessary.
  • Contains eggs. Free from gluten.

Nutritional Details (per serving)

These figures are for informational purposes only. Always consult a professional if needed.
  • Calorie Count: 216
  • Fat: 11 grams
  • Carbohydrates: 27 grams
  • Proteins: 7 grams