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.

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
Category | Breakfast, Snack, Fall Recipes |
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Prep Time | 10 minutes |
Cook Time | 20–22 minutes |
Servings | 12 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
- Preheat and Prep
Preheat your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease it. - Mix Wet Ingredients
In a large mixing bowl, whisk together pumpkin purée, eggs, Greek yogurt, honey, brown sugar, oil, and vanilla until smooth. - Combine Dry Ingredients
In a separate bowl, whisk flours, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger. - 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. - Fill the Muffin Pan
Divide the batter evenly among the muffin cups, filling each about ¾ full. - Bake
Bake for 20–22 minutes, or until a toothpick inserted in the center comes out clean. - 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.