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Three apple yogurt muffins stacked on top of each other. The muffins are wrapped in paper liners.
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5 from 4 votes

Apple Yogurt Muffins

These apple yogurt muffins are studded with apples and packed with cinnamon flavor. They're soft, fluffy and extra moist thanks to the Greek yogurt. Perfect for meal prep!
Prep Time10 minutes
Cook Time18 minutes
Total Time28 minutes
Course: Breakfast
Cuisine: American
Keyword: apple yogurt muffins
Servings: 12




  • Preheat oven to 400°F. Place 12 paper or silicone liners in your muffin tin.
  • In a large bowl, combine flour, baking powder, baking soda, salt and cinnamon.
    Mixing together flour, baking powder, baking soda, salt and cinnamon.
  • In a medium mixing bowl, whisk together eggs, Greek yogurt, oil, maple syrup, almond milk and vanilla extract.
  • Pour the liquid mixture into the bowl with the dry ingredients and stir until mixture is just combined. Don’t over-mix! It's okay if there are a few streaks of flour left.
    Adding wet ingredients to dry ingredients.
  • Fold in apple chunks.
    Folding in apples into the yogurt muffin batter.
  • Evenly divide the batter into the prepared muffin tins.
    Apple yogurt muffin batter divided into muffin tin with paper liners.
  • Bake for 16-18 minutes or until a toothpick inserted in the center of the muffin comes out clean.
    Twelve baked apple yogurt muffins in a muffin tin.
  • Let muffins cool in the tin for a few minutes, then remove so they don’t continue to cook and let cool completely on a wire rack.
  • Store at room temperature for 3-4 days or in the refrigerator for up to 1 week in an airtight container. You can also freeze for up to 3 months in a freezer-safe container.


  • Whole wheat pastry flour: If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • Greek yogurt: I haven’t tried it, but I bet using a vegan yogurt would work just fine! 
  • Maple syrup: You can use agave, honey or even monk fruit maple syrup as a substitute for maple syrup. 
  • Almond milk: Any dairy-free or dairy milk will work in this recipe.


Serving: 1muffin | Calories: 209kcal | Carbohydrates: 33g | Protein: 6g | Fat: 7g | Saturated Fat: 5g | Monounsaturated Fat: 1g | Cholesterol: 34mg | Sodium: 182mg | Potassium: 56mg | Fiber: 4g | Sugar: 10g