Looking for a healthy muffin recipe that’s easy to make and packed with flavor? These Greek Yogurt Muffins are naturally sweetened, made with whole wheat flour, and have a soft, fluffy texture.
Why You’ll Love These Healthy Muffins
- No refined sugar – naturally sweetened with honey & raisins.
- High in protein – thanks to Greek yogurt.
- Whole wheat + oats = fiber-rich and filling.
Ingredients for Greek Yogurt Muffins (12 muffins)
- 1 ½ cups whole wheat flour
- ½ cup rolled oats
- 1 tsp baking powder
- ½ tsp baking soda
- ½ tsp cinnamon
- ½ cup Greek yogurt or kefir (plain, full-fat or low-fat)
- ¼ cup maple syrup or honey
- ¼ cup coconut oil or melted butter
- 2 eggs
- 1 tsp vanilla extract
- ½ cup milk (any type)
- ¾ cup raisins (soaked in warm water for 10 minutes, then drained)
Step-by-Step Instructions
- Preheat oven to 350°F (175°C) and line a muffin tin.
- In a bowl, whisk together flour, oats, baking powder, baking soda, and cinnamon.
- In another bowl, mix Greek yogurt, maple syrup, coconut oil, eggs, vanilla, and milk until smooth.
- Combine the wet and dry ingredients, stirring gently.
- Fold in the raisins (drain them first if they were soaked).
- Divide the batter into muffin cups, filling each about ¾ full.
- Bake for 18-22 minutes or until a toothpick comes out clean.
- Let cool for 5 minutes before removing from the pan.
Substitutions for Greek Yogurt Muffins
- Greek Yogurt: Can replace with kefir or regular yogurt.
- Whole Wheat Flour: Can use all-purpose or a GF blend.
- Raisins: Swap for chocolate chips or dried cranberries.
- Coconut Oil: Use melted butter or olive oil instead.

Benefits of Greek Yogurt Muffins
These Greek Yogurt Muffins aren’t just delicious—they’re packed with health benefits, making them a great choice for breakfast, snacks, or lunchboxes.
Naturally Sweetened (No Refined Sugar!)
- Sweetened with honey and raisins, these muffins skip processed sugar while still being deliciously sweet.
- Perfect for kids and adults looking for a healthier treat.
Whole Wheat & Oats = More Fiber
- Made with whole wheat flour and oats for extra fiber, which helps with digestion and keeps energy levels steady.
- Great for a filling breakfast or a healthy snack.
Soft, Moist, and Kid-Approved
- The combination of Greek yogurt and coconut oil makes these muffins extra soft and fluffy.
- Kids love the natural sweetness of raisins—no need for extra sugar!
Easy to Make & Freezer-Friendly
- One-bowl recipe = minimal mess and quick prep.
- Make a batch and freeze them for up to 3 months—just reheat and enjoy!

Expert Tips for the Best Greek Yogurt Muffins
- Soak Raisins for Extra Moisture – Soak in warm water (or juice) for 10 minutes to keep them plump.
- Don’t Overmix – Stir just until combined to keep muffins light and fluffy.
- Use Full-Fat Greek Yogurt – Adds richness and moisture; if using low-fat, add a little oil.
- Toss Raisins in Flour – Prevents them from sinking in the batter.
- Fill Muffin Cups ¾ Full – Ensures the perfect dome shape.
- Bake at 350°F (175°C) for 18-22 Minutes – Use the toothpick test for doneness.
- Let Muffins Cool – Rest for 5 minutes in the pan before transferring to a wire rack.
- Store & Freeze – Keep in an airtight container for 3 days or freeze for up to 3 months.
FAQ
Q1. Can I make these Greek yogurt muffins without eggs?
Yes! You can substitute each egg with:
- 1 flax egg (1 tbsp ground flaxseed + 3 tbsp water, let sit for 5 minutes)
- ¼ cup unsweetened applesauce
- ¼ cup mashed banana (adds extra sweetness)
Q2. Can I use regular yogurt instead of Greek yogurt?
Yes, but since regular yogurt is thinner, reduce the milk slightly to maintain the right batter consistency.
Q3. Can I make these muffins gluten-free?
Absolutely! Swap the whole wheat flour for:
- A 1:1 gluten-free flour blend
- Oat flour (but muffins may be slightly denser)
Q4. How do I store these muffins?
- At room temperature: Store in an airtight container for up to 3 days.
- In the fridge: Keep for up to a week, but let them come to room temp before eating.
- In the freezer: Store in a freezer-safe bag for up to 3 months. Thaw overnight or microwave for 20-30 seconds before eating.
Q5. Can I use a different sweetener instead of honey or maple syrup?
Yes! You can use:
- Coconut sugar (same amount)
- Date syrup
- Mashed banana (reduce the milk slightly)
Q6. Can I use chocolate chips instead of raisins?
Definitely! Swap raisins for chocolate chips, dried cranberries, or chopped nuts for a fun variation.
Q7. Why are my muffins dense or dry?
- Overmixing the batter can make them tough. Stir until just combined.
- Not enough moisture—Make sure you’re using full-fat Greek yogurt and soaking the raisins.
- Overbaking—Check for doneness at 18 minutes with a toothpick.
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Healthy Greek Yogurt Muffins – No Refined Sugar!
Equipment
- 1 mixing bowl
- 1 muffin baking tray
Ingredients
- 1 ½ cups whole wheat flour
- 1/2 cup rolled oats
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp cinnamon
- pinch of salt
- 1/2 cup plain Greek yogurt (or kefir)
- 1/4 cup maple syrup (or honey)
- 1/4 cup melted coconut oil (or melted butter)
- 2 eggs
- 1 tsp vanilla extract
- 1/2 cup milk (any type)
- 3/4 cup raisins (soaked in warm water for 10 minutes, then drained)
Instructions
- Preheat oven to 350°F (175°C) and line a muffin tin.
- In a bowl, whisk together flour, oats, baking powder, baking soda, and cinnamon.
- In another bowl, mix Greek yogurt, maple syrup, coconut oil, eggs, vanilla, and milk until smooth. Combine the wet and dry ingredients, stirring gently.
- Fold in the raisins (drain them first if they were soaked).
- Divide the batter into muffin cups, filling each about ¾ full.
- Bake for 18-22 minutes or until a toothpick comes out clean.Let cool for 5 minutes before removing from the pan.
Notes
- The calories and macronutrients may vary slightly depending on ingredient brands.
- If using low-fat Greek yogurt, total fat will be lower.
- Adding chocolate chips or nuts will increase calories & fat content.