Healthy Greek Yogurt Pumpkin Muffins | Easy Fall Breakfast Recipe

There’s nothing quite like the cozy smell of pumpkin muffins baking in the oven on a crisp fall morning. These Healthy Greek Yogurt Pumpkin Muffins are soft, moist, and filled with warm autumn flavors—perfect for breakfast, a snack, or even lunchbox treats. Using Greek yogurt makes them extra fluffy and adds a little protein boost, so you can feel good about serving them to kids and adults alike.

Freshly baked healthy Greek yogurt pumpkin muffins cooling on a wire rack.

This recipe is simple enough for beginner bakers and uses pantry-friendly ingredients you likely already have. It’s one of those comforting recipes that feels like a hug in muffin form.

Recipe Info

CategoryBreakfast, Snack, Fall Recipes
Prep Time10 minutes
Cook Time20–22 minutes
Servings12 muffins
Calories~160 per muffin

Ingredients You’ll Need

  • 1 cup pumpkin purée (not pumpkin pie filling)
  • 2 large eggs
  • 1 cup plain Greek yogurt
  • ½ cup honey or pure maple syrup
  • ¼ cup light brown sugar, packed
  • ⅓ cup vegetable oil or melted coconut oil
  • 1 ½ cups all-purpose flour
  • ½ cup whole wheat flour (or use all all-purpose)
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • 1 teaspoon ground cinnamon
  • ½ teaspoon ground nutmeg
  • ¼ teaspoon ground cloves
  • ¼ teaspoon ground ginger
  • 1 teaspoon vanilla extract

Step-By-Step Instructions

  1. Preheat and Prep
    Preheat your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease it.
  2. Mix Wet Ingredients
    In a large mixing bowl, whisk together pumpkin purée, eggs, Greek yogurt, honey, brown sugar, oil, and vanilla until smooth.
  3. Combine Dry Ingredients
    In a separate bowl, whisk flours, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger.
  4. Bring It Together
    Gradually fold the dry mixture into the wet mixture. Stir until just combined—don’t overmix, or your muffins may turn dense.
  5. Fill the Muffin Pan
    Divide the batter evenly among the muffin cups, filling each about ¾ full.
  6. Bake
    Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean.
  7. Cool & Enjoy
    Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack. Serve warm or at room temperature.

Helpful Notes & Tips

  • Storage: Store muffins in an airtight container at room temperature for up to 3 days, or refrigerate for up to a week. They also freeze beautifully—just thaw overnight.
  • Moisture Tip: Don’t skip the Greek yogurt—it keeps the muffins extra tender.
  • Sweetness Adjustments: For less sweet muffins, reduce the brown sugar or swap honey for unsweetened applesauce.

Recipe Variations

  • Chocolate Chip Pumpkin Muffins: Stir in ½ cup mini chocolate chips before baking.
  • Nutty Crunch Muffins: Add ½ cup chopped walnuts or pecans for extra crunch.
  • Whole Grain Muffins: Use entirely whole wheat flour for a heartier, denser muffin.
  • Kid-Friendly Mini Muffins: Divide batter into a mini muffin tin and bake for 10–12 minutes.

Serving Suggestions

  • Serve warm with a pat of butter or drizzle of honey.
  • Pair with a cup of hot coffee, chai tea, or warm apple cider for a cozy breakfast.
  • Pack into lunchboxes for an easy fall snack.
  • Top with a dollop of Greek yogurt and a sprinkle of cinnamon for a protein-packed treat.

Conclusion

These Healthy Greek Yogurt Pumpkin Muffins are the perfect blend of cozy fall flavor and everyday simplicity. They’re easy enough to whip up on a weekday morning and wholesome enough to share with the whole family. Bake a batch, enjoy the warm pumpkin spice aroma, and savor each bite with someone you love.