Healthy Pumpkin Cream Cheese Muffins
Yields: 12 muffins
These tender muffins taste just like the irresistible ones from Starbucks, but they’re much healthier! They’re full of pumpkin, cozy spices, and plenty of cream cheese filling. They’ll keep for at least one week if stored in an airtight container in the refrigerator. And I highly recommend pairing them with my ultimate healthy pumpkin spice latte!
  • for the filling
  • 6 tbsp (90g) plain nonfat Greek yogurt
  • 6 tbsp (84g) Greek yogurt cream cheese, softened
  • ½ tsp liquid stevia, or adjusted to taste
  • ¼ tsp vanilla extract
  • for the muffins
  • 2 cups (240g) white whole wheat flour or gluten-free* flour (measured like this)
  • 1 tbsp (8g) ground cinnamon
  • ¼ tsp ground nutmeg
  • ¼ tsp ground ginger
  • 1 ½ tsp baking powder
  • ½ tsp baking soda
  • ½ tsp salt
  • 1 tbsp (14g) unsalted butter or coconut oil, melted and cooled slightly
  • 2 large egg whites, room temperature
  • 1 ½ tsp vanilla extract
  • 1 ½ tsp liquid stevia
  • ¼ cup (60g) plain nonfat Greek yogurt
  • 1 cup (244g) pumpkin purée, room temperature (not pumpkin pie mix)
  • ½ cup (120mL) nonfat milk
  1. Preheat the oven to 350°F, and lightly coat 12 muffin cups with nonstick cooking spray.
  2. To prepare the filling, beat the Greek yogurt and Greek yogurt cream cheese with a mixer until smooth and creamy. Add in the liquid stevia and vanilla. Beat until fully incorporated. Transfer to a zip-topped plastic bag.
  3. To prepare the muffin batter, whisk together the flour, cinnamon, nutmeg, ginger, baking powder, baking soda, and salt in a medium bowl. In a separate bowl, whisk together the butter, egg whites, vanilla, and liquid stevia. Stir in the Greek yogurt, mixing until no large lumps remain. Stir in the pumpkin purée. Alternate between adding the flour mixture and milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.)
  4. Evenly divide the batter between the prepared muffin cups. Cut the corner off of the zip-topped bag with the filling, and pipe the filling into the center of each muffin cup’s batter. (It’s okay if the filling sticks up over the top of the batter. The batter will rise around its sides as it bakes.) Bake at 350°F for 20-23 minutes or until the pumpkin parts of the tops feels firm to the touch and a toothpick inserted into the pumpkin part comes out clean. Cool in the muffin cups for 10 minutes before transferring to a wire rack.
Notes: For the best results, use block-style cream cheese, rather than tub-style cream cheese. Neufchâtel (⅓-less fat) cream cheese, regular cream cheese, and fat-free cream cheese may all be substituted for the Greek yogurt cream cheese, as long as they have been well softened.

Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.

For a stronger spice flavor, increase the cinnamon by up to an additional 1 teaspoon.

Any oil may be substituted for the unsalted butter or coconut oil.

I highly recommend using the liquid stevia! It’s my favorite sweetener, and you’ll use it in all of these recipes of mine, too. I buy mine online here because that's the best price I've found. If you prefer, 8-12 tablespoons of pure maple syrup, honey, or agave may be substituted for the liquid stevia in the muffin batter. If using this substitution, omit the milk. The baking time may change.

For a sweeter filling, increase the liquid stevia by ¼ to ½ teaspoon. If you prefer to substitute something else for the liquid stevia in the filling, then I recommend 1½ tablespoons of this powdered stevia or 8-12 tablespoons of granulated sugar. I don’t recommend using a liquid sweetener like pure maple syrup, honey, or agave because it will make the filling too runny.

Any milk may be substituted in place of the nonfat milk.

GLUTEN-FREE VERSION: For the gluten-free flour, I recommend the following blend: 1 cup (120g) millet flour, ½ cup (60g) brown rice flour, ½ cup (60g) tapioca flour, and 1 ½ teaspoons xanthan gum. Most store-bought gluten-free flour blends (like this one!) will work as well, if measured like this.

{gluten-free, clean eating, low fat, lower sugar, higher protein}
Recipe by Amy's Healthy Baking at