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A batch of golden blueberry muffins with juicy berries peeking through, served on a rustic tray with a side of fresh blueberries.

Healthier Blueberry Muffins Recipe – Naturally Sweet Muffins with Greek Yogurt & Whole Wheat Flour

These Healthier Blueberry Muffins are soft, moist, and bursting with juicy blueberries—made with better-for-you ingredients like whole wheat flour, Greek yogurt, and maple syrup. They’re naturally sweetened, lower in sugar, and perfect for breakfast, brunch, or snack time. Easy to make and freezer-friendly, these muffins deliver bakery-style flavor with a wholesome twist. Whether you're meal prepping or baking for the family, this recipe is a delicious way to enjoy a classic treat without the guilt.
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Breakfast, Brunch, Snack
Cuisine American, Healthy Baking
Servings 12 standard muffins
Calories 180 kcal

Equipment

  • Muffin tin
  • Paper or parchment liners
  • Mixing bowls
  • Whisk and spatula
  • Measuring Cups and Spoons
  • Ice cream scoop (optional)

Ingredients
  

Dry Ingredients:

  • 1½ cups whole wheat flour
  • 1 tsp baking powder
  • ½ tsp baking soda
  • ¼ tsp salt
  • ½ tsp cinnamon (optional)

Wet Ingredients:

  • ⅓ cup honey or maple syrup
  • ½ cup Greek yogurt or mashed banana
  • ¼ cup avocado oil or melted coconut oil
  • 2 large eggs (or flax eggs for vegan)
  • 1 tsp vanilla extract

Add-ins:

  • 1 cup blueberries (fresh or frozen)
  • 1 tbsp flour (for tossing blueberries)

Instructions
 

  • Preheat oven to 375°F (190°C). Line muffin tin with parchment or paper liners.
  • Mix dry ingredients in a large bowl: flour, baking powder, baking soda, salt, and cinnamon.
  • Mix wet ingredients in a separate bowl: honey/maple syrup, yogurt/banana, oil, eggs, and vanilla.
  • Combine wet and dry ingredients gently. Do not overmix.
  • Toss blueberries in 1 tbsp flour, then fold into batter.
  • Portion batter evenly into muffin cups, filling about ¾ full.
  • Bake for 18–22 minutes, until tops are golden and a toothpick comes out clean.
  • Cool in pan for 5 minutes, then transfer to a wire rack.
  • Store in airtight container for 3–4 days or freeze individually.

Notes

  • Use oat or almond flour for gluten-free options.
  • Substitute flax eggs and plant-based yogurt for a vegan version.
  • Add lemon zest, chia seeds, or chopped nuts for extra flavor and texture.
  • Frozen blueberries work well—no need to thaw.
  • Let batter rest 10–15 minutes before baking for better rise.
 
Keyword blueberry, freezer-friendly, healthy muffins, Kid-Friendly, refined sugar-free, whole wheat