There’s something about a warm blueberry muffin that just feels like home and these blueberry muffins with Greek yogurt have that bakery-style texture everyone loves but with a wholesome twist! They’re gluten-free, lower sugar, and higher protein than the traditional ones you'd grab from the store. These are the muffins you'll be able to whip up on a Sunday morning, toss in the freezer for busy weekdays, or pack in your little one’s lunchbox without a second thought.
Why You and Your Kids Will Love These Blueberry Muffins
- soft, fluffy, and not too sweet — just the right texture for little mouths (and grown-up taste buds)
- protein-packed thanks to Greek yogurt, which helps keep kids full longer and supports steady energy
- easy to make gluten-free and lower in sugar by lightly sweetening with maple syrup or using mashed banana
- perfect for meal prep — they freeze beautifully and reheat soft, making weekday breakfasts a breeze
- lunchbox and snack approved — no crumbs everywhere, just tender muffin goodness that holds together
If you want a little extra *boosted* muffin recipe, then check out my lemon blueberry chickpea muffins and my pumpkin chickpea muffins for extra protein + fiber!
Jump to:
- Why You and Your Kids Will Love These Blueberry Muffins
- Ingredients You'll Need
- How To Make Your Blueberry Muffins With Greek Yogurt
- Hint For The Best Blueberry Muffins
- Substitutions
- Variations
- Equipment
- Storing Your Blueberry Muffins
- Tiff's Dietitian Tip
- FAQ
- Related
- Pairing
- Blueberry Muffins with Greek Yogurt (low sugar & kid-friendly)
Ingredients You'll Need
Here's what you'll need to make these blueberry muffins with Greek yogurt:
- gluten-free 1:1 baking flour or all-purpose flour: I love using King Arthur Measure for Measure or Bob’s Red Mill 1:1, both bake up light and fluffy, not gummy like some gluten-free blends (feel free to use any all-purpose flour)
- baking powder + baking soda: this combo helps the muffins rise tall with that perfect bakery-style dome
- salt: just a pinch brings out the sweetness and balances the flavor
- Greek yogurt: the secret to these muffins’ soft, moist texture! it adds protein, helps them stay fresh longer, and gives a subtle tang that pairs beautifully with blueberries
- milk: thins the batter just enough, any milk works here (dairy or dairy-free)
- maple syrup or honey: light sweetness that keeps the muffins refined sugar–free while adding moisture
- melted butter or olive oil: adds richness and that classic bakery crumb
- eggs: provide structure and help the muffins rise (see the vegan swaps below if you’re egg-free)
- vanilla extract: a must for warm, bakery-style flavor
- blueberries: fresh or frozen either works, tossing them in flour keeps them evenly distributed
- coconut or brown sugar (optional): a sprinkle on top gives that crisp, golden bakery look and a little sparkle
See recipe card for quantities.
How To Make Your Blueberry Muffins With Greek Yogurt
- Step 1: In a large bowl, whisk together the flour, baking powder, baking soda, and salt.
- Step 2: Then stir in the Greek yogurt, milk, maple syrup (or honey), melted butter or oil, eggs, and vanilla until smooth.
- Step 3: Fold in the blueberries (tossed in a little flour to prevent sinking). Divide the batter evenly into a lined muffin tin, filling each cup about ¾ full. Sprinkle with coconut or brown sugar if using.
- Step 4: Bake at 350°F for 12-15 minutes, or until the tops are golden and a toothpick comes out clean. Let cool 5-10 minutes before serving.
Hint For The Best Blueberry Muffins
For lifted, bakery-style muffin tops, let the batter rest for 10-15 minutes before baking, it’s the secret to that perfect dome!
Substitutions
These blueberry muffins with Greek yogurt are already gluten-free if using gluten-free flour, and can easily be adjusted for other dietary restrictions!
- dairy-free: swap greek yogurt for ½ cup unsweetened coconut yogurt (or another thick plant-based yogurt). use coconut milk or almond milk instead of dairy milk (or any dairy-free milk of choice), and replace butter with melted coconut oil or avocado oil
- egg-free: replace each egg with ¼ cup unsweetened applesauce (½ cup total) or make flax eggs (2 tablespoon ground flax + 6 tablespoon water, rest 5 minutes), add ½ teaspoon apple cider vinegar to your wet ingredients to help the muffins rise better without eggs
- no added sugar: skip the maple syrup or honey and use 1-2 mashed ripe bananas or ½ cup unsweetened applesauce instead, the muffins will still be lightly sweet with natural fruit flavor (might need to add a little extra milk if the batter is too thick)
- extra fiber: stir in 2 tablespoon ground flaxseed, chia seeds, or Tiny Sprouts brain booster for a subtle boost of fiber and healthy fats! you can also replace ¼ cup of the flour with oat flour for extra texture and staying power
Variations
Feel free to add different mix-ins into this blueberry muffin recipe or even sub out the blueberries for a completely different muffin flavor!
- lemon blueberry muffins: add 1 tablespoon lemon zest and 1 tablespoon lemon juice to the batter for a bright, bakery-style flavor that pairs perfectly with greek yogurt
- banana blueberry muffins: replace half of the greek yogurt with ½ cup mashed ripe banana for extra sweetness and a soft, cake-like texture
- mixed berry muffins: swap some of the blueberries for chopped strawberries, raspberries, or blackberries for a colorful, antioxidant-packed batch
- blueberry oat muffins: fold in ½ cup quick oats for added texture and fiber — they make the muffins extra hearty and filling for breakfast
- chocolate chip blueberry muffins: mix in 2-3 tablespoon mini chocolate chips for a fun twist that kids love
- zucchini blueberry muffins: add ½ cup finely shredded zucchini (squeezed dry) for a sneaky veggie boost
Equipment
You don’t need anything fancy to make these blueberry muffins with Greek yogurt, just a few basics you probably already have in your kitchen! Grab a mixing bowl, a whisk, a spatula, and a 24-cup mini muffin tin (or silicone muffin pan for easy cleanup). Use paper liners or a little oil spray to prevent sticking if desired. A cookie scoop makes it easy to portion the batter evenly so every muffin bakes up the same size and rises perfectly.
Storing Your Blueberry Muffins
Store these blueberry muffins in an airtight container at room temperature for up to 3 days, or in the fridge for 5-6 days. Just warm them in the microwave for a few seconds to bring back that fresh-from-the-oven feel. To freeze, let the muffins cool completely, then place them in a freezer-safe bag or container for up to 3 months. When you’re ready to enjoy, microwave straight from frozen for about 20–30 seconds or pop them in a 300°F oven for a few minutes until warm. I love keeping a few on hand for quick toddler breakfasts, they pair perfectly with fruit and yogurt for an easy, balanced meal!
Tiff's Dietitian Tip
Greek yogurt adds more than just moisture, it gives these muffins a boost of protein and calcium to help keep kids satisfied and support strong bones and muscles. Pairing a muffin with fruit and milk or yogurt helps create a balanced meal that covers all the bases: carbs for energy, protein for staying power, and healthy fats for fullness. If you’re serving these as a snack, try adding a few hemp hearts or nut butter on the side for an extra nutrient boost!
FAQ
Absolutely. Use unsweetened coconut or almond yogurt in place of Greek yogurt, dairy-free milk instead of regular milk, and melted coconut oil or avocado oil instead of butter.
Yes, replace the eggs with ½ cup unsweetened applesauce or 2 flax eggs (2 tablespoons ground flax + 6 tablespoons water). Add ½ teaspoon apple cider vinegar to help them rise just like the egg version.
Yes! Scoop the batter into a standard muffin tin and bake at 350°F for 20-22 minutes, or until the tops are golden and a toothpick comes out clean. Let them cool for at least 5-10 minutes before removing from the pan.
Related
Looking for other recipes like this? Try these:
Pairing
These are my favorite dishes to serve with this toddler-friendly blueberry muffin recipe:
Blueberry Muffins with Greek Yogurt (low sugar & kid-friendly)
Ingredients
- 2 cups all-purpose flour or gluten-free 1:1 baking flour king arthur measure for measure or bob’s red mill 1:1
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- ¼ teaspoon salt
- ½ cup plain greek yogurt or thick dairy-free if needed
- ½ cup milk dairy or non-dairy
- ¼ cup maple syrup or honey ⅓ cup for more sweet or sub with ripe mashed banana or applesauce for no added sugar
- ¼ cup melted butter or olive oil
- 2 large eggs or sub with flax eggs
- 1½ teaspoons vanilla extract
- 1 cup fresh or frozen blueberries personally love frozen wild blueberries
- coconut or brown sugar optional for sprinkling on top
Instructions
- Preheat oven to 350°F and line a mini muffin tin (you’ll need 2-3 trays or bake in batches) with paper liners or grease well.
- In a large bowl, whisk the flour, baking powder, baking soda, and salt. Mix in the Greek yogurt, milk, maple syrup (or honey), melted butter or oil, eggs, and vanilla until smooth.
- Fold in the blueberries by gently mixing in.
- Scoop the batter into the mini muffin cups, filling each about ¾ full. Sprinkle with coconut sugar if using.
- Bake for 12-14 minutes, or until the tops are lightly golden and a toothpick comes out clean.
- Let the muffins cool for 5 minutes in the pan before transferring to a wire rack.
Sarah R says
Unreal. No words. 🙂
toddlerdietitiantiff says
hehehe they're our favorite!!
Ches says
How are these so good? 😲 It sounds like any other muffin, but it's not. Too good. Definitely need to make 2-3 batches a week!
toddlerdietitiantiff says
YAY!! So glad y'all loved them! They disappear really fast in our house too😂
Anna says
Made these yesterday. So easy and so good! We used frozen blueberries since Blueberries aren’t in season. I also did a variety of mini muffins, a few regular size muffins and a few donut shaped muffins.
Toni says
Hi there! For the frozen blueberries m, do you need to completely defrost and drain?
toddlerdietitiantiff says
nope!! I just stick them in frozen!