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Healthy Chocolate Chip Pumpkin Protein Muffin on white plate with broken piece beside to show texture

Healthy Pumpkin Chocolate Chip Protein Muffins (Bakery-Style & 7g Protein)

Soft pumpkin chocolate chip muffins made with Greek yogurt and pumpkin puree. This healthy pumpkin muffin recipe is easy to make, freezer-friendly, and perfect for fall baking.
Prep Time 15 minutes
Cook Time 30 minutes
Cooling Time 10 minutes
Total Time 55 minutes
Serving Size 12 Muffins
Calories: 220kcal

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.
    Parchment-lined muffin cups

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
    Pumpkin puree, Greek yogurt, egg whites, maple syrup, and applesauce being whisked together in a mixing bowl

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
    Flour, pumpkin pie spice, cinnamon, baking powder, and baking soda mixed in a bowl

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.
    Pumpkin muffin batter mixed and ready for chocolate chips

Add Chocolate Chips

  • Fold in the chocolate chips.
    ¾ cup dark chocolate chips
    Healthy pumpkin chocolate chip muffin batter with chocolate chips folded in

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
    Healthy pumpkin chocolate chip muffin batter divided into parchment-lined muffin cups

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.
    Pumpkin chocolate chip muffins topped with extra chocolate chips before baking

Cool

  • Allow muffins to cool in the pan for 10 minutes before transferring to a wire rack.
    Bakery-style healthy pumpkin chocolate chip protein muffins cooling on 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.
Estimated Macros:
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.