These healthy chocolate chip muffins with oats are moist and fluffy and go fast! Made with gluten-free flour, oats, monk fruit (Xylitol or coconut sugar), and little oil. They are a sure bet everyone will enjoy this healthy twist! They start from the same well method as my homemade muffin base.

You'll never believe these fluffy, moist, muffins are actually good for you! We make 12 muffins and they are gone in a day! Add them to your morning routine along with baked oats, overnight chia pudding, healthy chocolate chip bread loaf, and these healthy oatmeal muffins.
Quick Look
- 🕒 Prep Time: 10 minutes
- 🌡️ Cook Time: 18 minutes at 400 degrees F
- ⏳ Total Time: 28 minutes
- 🍽️ Serving: 12 muffins
- ⚡ Calories: 183kcal per muffin
- 🥣 Ingredients: 11, including gluten-free flour, quick oats, Greek yogurt and chocolate chips
- 🌶️ Flavor Profile: Soft, fluffy oat muffins with pockets of melty chocolate and a golden top
- ✋ Difficulty: One bowl, fold in the chips, rest the batter 5 minutes, bake
Quick Answer
Preheat the oven to 400 degrees F and line a muffin tin. Whisk ½ cup Greek yogurt, ½ cup non-dairy milk, 1 large egg and 1 teaspoon vanilla, then add 1 cup gluten-free flour, ¾ cup quick cook oats, ⅔ cup monk fruit or coconut sugar, 1 tablespoon baking powder, ¾ teaspoon salt and ¼ cup melted coconut oil and combine well. Fold in 1 cup of chocolate chips and let the batter set for 5 minutes. Scoop the batter into the muffin cups about ¾ full and bake 18 to 20 minutes until golden on top and a toothpick comes out clean. Makes 12 muffins at 183 calories each.
Jump to:
- Quick Look
- Quick Answer
- Why These Muffins Work
- Why You'll Love These Muffins
- Key Ingredients
- Health Benefits of Chocolate Chips
- How to Make Healthy Chocolate Chip Muffins
- Expert Tips
- Storing and Freezing Muffins
- Healthy Chocolate Chip Muffin FAQs
- More Healthy Muffin Recipes
- Healthy Chocolate Chip Muffins Recipe
You'll never believe these fluffy, moist, muffins are actually good for you! They are made with gluten-free flour and oats, yogurt for moisture, minimal oil, and sweetened with natural sugars.
Watch this short video on making these chocolate chip muffins:
Why These Muffins Work
Click to see why it works
- Yogurt brings the moisture. Greek yogurt and non-dairy milk keep these muffins light and fluffy without the guilt of extra fat.
- Oats add body. Gluten-free quick cook oats give the muffins structure and a tender crumb alongside the gluten-free flour.
- Resting the batter matters. Letting the batter set for 5 minutes gives the oats time to absorb liquid before baking.
- Room temperature ingredients. Eggs and milk used at room temperature help hold muffins together and keep them fluffy.
- Natural sweetness. Monk fruit is a natural sugar that does not spike blood sugar, and coconut sugar works too.
- A hot oven for a golden top. Baking at 400 degrees F for 18 to 20 minutes sets a golden dome while the center stays soft.
Why You'll Love These Muffins
- Moist and fluffy, and they go fast. We make 12 muffins and they are gone in a day!
- Made with better ingredients: gluten-free flour, oats, yogurt for moisture, minimal oil, and natural sugars.
- 183 calories each, ready in 28 minutes.
- Easy to make dairy-free with coconut yogurt, non-dairy milk and dairy-free chocolate chips.
- Part of the muffin family with my oatmeal blueberry muffins, apple muffins and chocolate chip spinach muffins.
Key Ingredients

- Gluten-free flour blend - we tested and suggest Bob's Red Mill 1-1 Mix. If gluten is not an issue, you can also use spelt flour or whole wheat flour.
- Gluten-free oats - make sure they are certified gluten-free for a gluten sensitivity.
- Greek yogurt - or plain coconut yogurt for dairy-free.
- Coconut sugar or monk fruit sugar - monk fruit is a natural sugar that does not spike blood sugar.
- Coconut oil or avocado oil - if using coconut oil, melt it first.
- Egg, baking powder and vanilla extract - the classic muffin lift and flavor.
- Pink salt - pink Himalayan salt is loaded with trace minerals. You can also use table salt.
- Chocolate chip morsels - or chocolate chunks, dark chocolate morsels, or vegan dairy-free chocolate chips.
See recipe card for quantities.
Health Benefits of Chocolate Chips
Did you know chocolate can boost your mood and reduce symptoms of depression? Dark chocolate is high in magnesium and anandamide, which enhances mood. And there are many more health benefits of chocolate.
Cocoa in chocolate is packed with a wonderful antioxidant called flavanol. Flavanol helps boost brain power, prevents ageing, and can lower cholesterol. The fact that it can lower cholesterol boggled my mind since chocolate is full of fat. But cocoa has plant sterols, which increase flexibility of veins and arteries helping to push blood through your body more efficiently.
All being said, it is best to choose dark chocolate chips for making a healthier chocolate chip muffin.
How to Make Healthy Chocolate Chip Muffins
1Preheat and prep. Preheat the oven to 400 degrees F. Line a muffin tin with paper liners or spray a silicone muffin pan.

2Whisk the wet ingredients. In a mixing bowl, whisk together the egg, milk, yogurt and vanilla until blended.

3Add the dry ingredients. Add in the flour, oats, sugar, baking powder, salt and coconut oil and combine well.

4Fold in the chocolate. Carefully fold in 1 cup of chocolate chips. Let the batter set for 5 minutes.

5Fill the cups. Scoop batter into muffin cups about ¾ full.

6Bake. Bake 18-20 minutes until golden on top and a toothpick inserted comes out clean. Remove muffins from the pan and transfer to a cooling rack to cool.
As always, be sure to check out the full recipe details in the recipe card below.
Expert Tips
- Let the batter rest 5 minutes after folding in the chips so the oats absorb the liquid.
- Fill cups about ¾ full for a rounded top without overflow.
- Use room temperature dairy and eggs to keep the muffins light and fluffy.
- Choose dark chocolate chips for a healthier chocolate chip muffin.
- Swap the chips for fruit: in place of chocolate chips you can use fresh fruit such as blueberries, strawberries, or apple chunks.
- Reheat for 5-10 seconds in the microwave to make day-old muffins warm and fluffy again.
Storing and Freezing Muffins
Store these muffins in an airtight container on the counter. As they set they will harden slightly and can be reheated in the microwave for 5-10 seconds to make them warm and fluffy again. Consume within 3 days for the best taste.
Although these healthy chocolate chip muffins are best fresh, they can be frozen. To freeze muffins, wrap each one in wax paper and add it to a sealed freezer bag with the air removed for up to 3 months.
Be sure to try all of our Healthy Muffin Recipes, including gluten-free blueberry oat muffins and healthy oatmeal chia seed muffins.
Healthy Chocolate Chip Muffin FAQs
Muffins that are made with whole grains and natural sugars are the healthiest to eat. In place of chocolate chips you can use fresh fruit such as blueberries, strawberries, or apple chunks as a substitute.
Each of these muffins contains approximately 183 calories, with 22 grams of carbohydrates, 4 grams of protein, 9 grams of fat, 2 grams of fiber and 10 grams of sugar.
Dairy is the secret to making baked goods light and fluffy. Eggs, butter, and milk used at room temperature add moisture and help hold muffins together. We use yogurt and non-dairy milk to keep these light and fluffy without extra fat.
Yes. Use plain coconut yogurt in place of Greek yogurt, a non-dairy milk like almond, cashew or coconut milk, and dairy-free chocolate chips.
Store them in an airtight container on the counter and consume within 3 days. Reheat in the microwave for 5-10 seconds to make them warm and fluffy again.
Yes. Wrap each one in wax paper and add it to a sealed freezer bag with the air removed for up to 3 months.
More Healthy Muffin Recipes
Try our other healthy muffin recipes: Healthy Oatmeal Chia Seed Muffins, Apple Muffins, Healthy Gluten-Free Pumpkin Muffins, Gluten-Free Blueberry Oat Muffins and Chocolate Chip Spinach Muffins. If you make our healthy chocolate chip muffin recipe from Delightful Mom Food I would love to see your creations and share it! Follow along with me on Instagram, Pinterest, Facebook, YouTube and Twitter for a feature and more recipe inspiration! And don't forget to leave a comment below!

Healthy Chocolate Chip Muffins Recipe
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Ingredients
- ½ cup Greek yogurt or plain coconut yogurt
- ½ cup non-dairy milk almond milk, cashew milk, or coconut milk
- 1 large egg room temperature
- 1 teaspoon vanilla extract
- 1 cup gluten-free flour
- ¾ cup quick cook oats gluten-free
- ⅔ cup monk fruit or coconut sugar
- 1 tablespoon baking powder
- ¾ teaspoon salt
- ¼ cup coconut oil melted, or avocado oil
- 1 cup chocolate chips milk chocolate, dark chocolate, semi-sweet chocolate or dairy-free chocolate chips
Instructions
- Preheat the oven to 400 degrees F. Line a muffin tin with paper liners or spray a silicone muffin pan.
- In a mixing bowl add the yogurt, milk, egg, and vanilla and whisk together until blended. Add in the flour, oats, sugar, baking powder, salt and coconut oil and combine well.
- Carefully fold in 1 cup of chocolate chips. Let the batter set for 5 minutes.
- Scoop batter into muffin cups about ¾ full.
- Bake 18-20 minutes until golden on top and a toothpick inserted comes out clean. Remove muffins from the pan and transfer to a cooking rack to cool.















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