Healthy Pumpkin Chocolate Chip Protein Muffins (Bakery-Style & 7g Protein)
These healthy pumpkin chocolate chip protein muffins are soft, fluffy, and made with Greek yogurt, pumpkin puree, and chocolate chips. Each muffin has 7g of protein and a tall bakery-style muffin top.
QUICK LOOK: PUMPKIN CHOCOLATE CHIP MUFFINS
⏱️ Prep Time: 15 minutes
🔥 Bake Time: 30-35 minutes
🍽️ Servings: 12 bakery-style muffins
🔢 Calories: ~220 calories per muffin
💪 Protein: ~7g per muffin
💡 Difficulty: Easy
🎃 Key Ingredients: Pumpkin puree, Greek yogurt, egg whites, pumpkin pie spice, chocolate chips
🌾 Dietary Info: High protein, easily made gluten-free
❤️ Make Them For: Fall breakfasts, lunchboxes, meal prep, after-school snacks, Thanksgiving brunch
Every September, I promise myself I’ll hold off on pumpkin season for just a bit longer. Then I see that first can of pumpkin puree in the grocery store, and well… so much for waiting!
These healthy pumpkin chocolate chip muffins are soft, fluffy, and packed with warm fall spice and melty chocolate chips. They’re made entirely without refined sugar and get a real-food protein boost from plain Greek yogurt and egg whites, no protein powder required!
If your in fall baking mode too, be sure to check out my Pumpkin Spice Energy Balls, Pumpkin Spice Protein Mug Cake, Pumpkin Banana Yogurt Protein Bark, Pumpkin Spice Mummy Cookies, or Pumpkin Rice Krispie Treats for more easy morning and snack ideas.
And if you’re looking for more healthy muffin ideas, check out my Greek Yogurt Chocolate Chip Muffins next.
Why You’ll Love These Pumpkin Chocolate Chip Muffins
Key Ingredients Notes & Substitutions
Here’s a look at the main ingredients and easy substitutions. * For exact measurements and instructions, scroll down to the recipe card.
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Recommended Supplies/Tools
- Measuring cups and spoons
- Spoon or spatula
- Stand or hand Mixer
- 2 (12-count) muffin tins
How to Make Chocolate Chip Pumpkin Protein Muffins
Time needed: 55 minutes
- Prep
Preheat your oven to 425°F.
Line a 12-cup muffin pan with parchment liners, leaving an empty space between each muffin. Leaving space allows the muffins room to grow the taller bakery-style muffin tops.
- Mix the Wet Ingredients
Using a stand mixer fitted with the paddle attachment (or a large bowl with a hand mixer or whisk), combine the pumpkin puree, egg whites, whole egg, Greek yogurt, applesauce, maple syrup, coconut sugar, vanilla extract, and melted butter (or coconut oil). Mix for 2 to 3 minutes until smooth.
- Mix Dry Ingredients
In a separate bowl, stir together the flour, baking powder, baking soda, pumpkin pie spice, cinnamon, and salt until it’s all mixed well.
- Combine
Add the dry ingredients to the wet ingredients and stir just until combined. Avoid overmixing as this can activate the gluten and make the muffins tough or chewy.
- Add Chocolate Chips
Fold in the chocolate chips.
- Fill Muffin Cups
Fill each muffin cup all the way to the top with batter, right up to the rim of the liner. Unlike traditional cupcakes or small muffins that are filled two-thirds full, filling the liners completely is the secret to getting big, beautifully domed bakery-style muffin tops. Top with additional chocolate chips and coarse sugar, if desired.
- Bake
Bake at 425°F (218°C) for 5 minutes. Without opening the oven door, lower the heat to 350°F (175°C) and bake for an additional 25 to 30 minutes.
The initial burst of high heat triggers a rapid rise for those signature tall, domed tops, while lowering the temperature allows the centers to bake through evenly without burning the crust.
The muffins are done when a toothpick inserted into the center comes out clean or with a few moist crumbs.
- Cool
Allow muffins to cool in the pan for 10 minutes before transferring to a wire rack.
Healthy Pumpkin Chocolate Chip Protein Muffins (Bakery-Style & 7g Protein)
Ingredients
Wet Ingredients
- 1 cup pumpkin puree
- 5 egg whites
- 1 large egg
- ¾ cup plain Greek yogurt or blended cottage cheese
- ½ cup unsweetened applesauce
- ⅓ cup maple syrup
- ¼ cup coconut sugar
- 1 tsp vanilla extract
- 3 tbsp melted butter or coconut oil
Dry Ingredients
- 2 cups all-purpose flour I like to use organic unbleached, you can also use 1:1 gluten free all purpose blend
- 1 tsp baking powder
- ½ tsp baking soda
- 1½ tsp pumpkin pie spice
- 1 tsp cinnamon
- ½ tsp sea salt
Mix-Ins
- ¾ cup dark chocolate chips plus extra chocolate chips for topping
- Coarse sugar for topping optional
Instructions
Prep
- Preheat your oven to 425°F and line a 12-cup muffin pan with parchment liners, leaving an empty space between each muffin. Leaving space allows the muffins room to grow the taller bakery-style muffin tops.
Mix the Wet Ingredients
- Using a stand mixer fitted with the paddle attachment (or a large bowl with a hand mixer or whisk), combine the pumpkin puree, egg whites, whole egg, Greek yogurt, applesauce, maple syrup, coconut sugar, vanilla extract, and melted butter (or coconut oil). Mix for 2 to 3 minutes until smooth.1 cup pumpkin puree, 5 egg whites, 1 large egg, ¾ cup plain Greek yogurt, ½ cup unsweetened applesauce, ⅓ cup maple syrup, 1 tsp vanilla extract, 3 tbsp melted butter or coconut oil, ¼ cup coconut sugar
Mix the Dry Ingredients
- In a separate bowl, stir together the flour, baking powder, baking soda, pumpkin pie spice, cinnamon, and salt until it’s all mixed well.2 cups all-purpose flour, 1 tsp baking powder, ½ tsp baking soda, 1½ tsp pumpkin pie spice, 1 tsp cinnamon, ½ tsp sea salt
Combine
- Add the dry ingredients to the wet ingredients and stir just until combined. Avoid overmixing as this can activate the gluten and make the muffins tough or chewy.
Add Chocolate Chips
- Fold in the chocolate chips.¾ cup dark chocolate chips
Fill Muffin Cups
- Fill each muffin cup all the way to the top with batter, right up to the rim of the liner. Unlike traditional cupcakes or small muffins that are filled two-thirds full, filling the liners completely is the secret to getting big, beautifully domed bakery-style muffin tops. Top with additional chocolate chips and coarse sugar, if desired.Coarse sugar for topping
Bake
- Bake at 425°F (218°C) for 5 minutes. Without opening the oven door, lower the heat to 350°F (175°C) and bake for an additional 25 to 30 minutes. The initial burst of high heat triggers a rapid rise for those signature tall, domed tops, while lowering the temperature allows the centers to bake through evenly without burning the crust. The muffins are done when a toothpick inserted into the center comes out clean or with a few moist crumbs.
Cool
- Allow muffins to cool in the pan for 10 minutes before transferring to a wire rack.
Notes
- Use parchment liners because the muffins can stick to regular paper liners.
- Fill liners almost to the top for tall bakery-style muffin tops.
- Blended cottage cheese can be substituted for Greek yogurt.
- These muffins freeze well for up to 3 months.
Calories: 225 | Protein: 7g | Carbohydrates: 35g | Fat: 7g | Sugar:16g | Fiber: 3g Note: these are estimated and will vary based on ingredients and brands used.
Nutrition Information
Estimated Macros Per Serving Based on 16 Treats:
- Calories ~220
- Protein ~7g
- Carbohydrates ~35g
- Fiber ~3g*
- Sugar ~16g
- Fat ~6g
NOTE: Nutrition values are estimates and will vary depending on brands and ingredients used.
Trish’s Tips
- Measure flour accurately: Use the spoon-and-level method (use a spoon to add the flour into the measuring cup, and level it off with a knife) to keep the muffins light and soft rather than dense.
- Bake with room-temperature ingredients: Bring cold items like eggs, milk, and butter to room temperature so they emulsify smoothly and create a uniform texture.
- Avoid overmixing: Stir the wet and dry ingredients together just until combined; overworking the batter develops gluten, resulting in tough, heavy muffins.
- Start with a high oven temperature: Baking at an initial higher heat creates a rapid burst of steam that lifts the batter, yielding tall, bakery-style muffin tops.
- Use parchment liners: Line the muffin tin with parchment paper liners to prevent sticking, as they release more cleanly than standard paper cups.
- Add top toppings: Press a few extra chocolate chips or sprinkle coarse sugar onto the batter right before placing in the oven for a bakery-style finish.
Variations & Substitutions
Make Them Gluten-Free
Use a 1:1 gluten-free all-purpose flour blend.
Use Cottage Cheese
Blend cottage cheese until smooth and use it in place of Greek yogurt.
Add Nuts
Fold in chopped pecans or walnuts for extra crunch.
Add More Protein
Mix in 1-2 tablespoons of hemp hearts.
Standard Muffins
Make 24 standard muffins instead of 12 bakery-style muffins. Fill liners about ⅔ full and bake at 350°F for 20-25 minutes.
Looking for More Chocolate Chip Treats? Try One of These Recipes Next:
Frequently Asked Questions
Because these healthy pumpkin chocolate chip muffins contain less fat than traditional bakery muffins, they can stick to regular paper liners. For best results, use parchment paper liners, foil liners, or lightly spray your liners with cooking spray before filling.
Yes. A good quality 1:1 gluten-free flour blend works well in this recipe.
For best results, replace no more than ¼ to ½ cup of the flour with protein powder and use a protein powder you already enjoy baking with. You may also need to add a little extra liquid, such as Greek yogurt, milk, or pumpkin puree, to keep the muffins soft and moist. This pumpkin chocolate chip muffin recipe gets its protein from Greek yogurt, egg whites, and eggs, so there’s no need to add protein powder unless you’d like an extra protein boost.
