Healthy Greek Yogurt Mini Muffins with Chocolate Chips (No Refined Sugar)

Mini muffins are one of those things I always come back to. They work for breakfast, a quick snack, or even a little dessert. And the best part? These muffins are sweetened with honey instead of refined sugar and the rest of ingredients make for an excellent clean mini muffin, way better than the store bought ones! Once I started making these homemade mini muffins, my kids quit asking to buy the others!

I love using Greek yogurt in them because it keeps them soft and tender. I make my own yogurt in the crockpot, so that’s a double win! I usually make a HUGE batch of these homemade mini muffins and freeze the extras. They are so handy to pull out of the freezer.

If you want a muffin that works for dessert, snack, breakfast, or even a side on a brunch table, these Greek Yogurt Mini Muffins are it!

The Good Stuff Ingredient Swaps

While the full measurements are in the recipe card below, here is why I chose these specific “Good Stuff” ingredients for this recipe:

Whole Cell Crushed Wheat: You can use all-purpose, but I love using whole cell crushed wheat or fresh milled flour for the extra nutrients. Check out my guide on the best flour swaps here!

Whole Milk Greek Yogurt: This adds moisture and a serious protein boost. If you’re feeling ambitious, you can even use your own Homemade Yogurt.

Honey or Maple Syrup: We skip the refined white sugar and use these instead. I’ve found that swapping sugar for natural sweeteners not only tastes better but avoids that mid-morning sugar crash.

Real Vanilla Extract: Most store-bought vanillas are imitation “vanillin.” I always recommend using the real deal—you can see why in my Vanilla Simple Swap, or you can see how making your own vanillais actually incredibly easy.

Mini Chocolate Chips: I like using mini chips so you get a little chocolate in every bite without overdoing it, but regular chocolate chips will work also. For my favorite chocolate chips be sure to check out my chocolate chip swap!

A Note About the Flour

We use whole cell crushed wheat, any flour or fresh milled flour will work. Since this is a small amount of flour and a quick bread, we aren’t going to worry as much about weighing it. If you they come out a little dry, you can always reduce the flour by a hair for the next time.

Instructions

1. Preheat your oven to 375 degrees F and lightly grease a 24-cup mini muffin pan with nonstick spray.
2. In a medium bowl, mix the flour, baking powder, baking soda, and salt.
3. In another bowl, whisk together the Greek yogurt, honey, eggs, melted butter, and vanilla until smooth.
4. Pour the wet ingredients into the dry and fold gently until just combined. A few streaks of flour are fine- don’t overmix.
5. Stir in the chocolate chips so they’re evenly spread through the batter.
6. Spoon about 1 1/2 tablespoons of batter into each muffin cup, filling almost to the top.(see photos below)
7. Bake for 10-12 minutes until the edges turn lightly golden and a toothpick comes out clean. Watch closely so they don’t overbake.
8. Let the muffins cool in the pan for a couple of minutes, then carefully run a knife around the edges and transfer them to a wire rack to finish cooling.

Pre baked & after! Left to right: Chocolate Chip, Freeze Dried Strawberry, Blueberry & Sprinkles

Variations & Mix-Ins

These mini muffins with chocolate chips are super versatile. Once you know the base, you can swap in add-ins or mix-ins to make them your own. Here are some of my favorites:

• Peanut Butter Chocolate Chip: Replace 1 egg with 1/4 cup peanut butter for extra protein and flavor.
• Dye-Free Sprinkles: Perfect for birthdays or holidays.
• Dried Fruit: Raisins, cranberries, or chopped apricots make them extra snackable.
• Nuts & Seeds: Walnuts, pecans, or sunflower seeds add crunch.
• Cocoa or White Chocolate Chips: Swap half the chocolate chips for cocoa or white chocolate.
• Fresh Fruit: Blueberries, raspberries, or finely chopped apples. Reduce other liquids slightly if using juicy fruit.
• Spices: Cinnamon, pumpkin pie spice, or a pinch of nutmeg for a seasonal twist.

Honestly, once you have the base, the sky’s the limit. I love swapping things in depending on what I have on hand, the season, or what the kids are asking for.

More Mini Muffin Favorites

We love having a stash of healthy mini muffins so much that it was even a featured Good Stuff Simple Swap! For more mini muffins recipes you’ll want to check out these other favorites from the blog:

• Healthy Banana Chocolate Chip Mini Muffins with Greek Yogurt (No Refined Sugar): The perfect way to use up those brown bananas!
• Peanut Butter Protein Mini Muffins: For when you need an extra protein hit! This version uses peanut butter and protein powder to keep you full even longer.

FAQ

Can I make these gluten-free?
Yes. Use a 1-to-1 gluten-free flour blend. Baking time may vary slightly.

Can I make these dairy-free? Absolutely, just use a nondairy Greek style yogurt and avocado oil in place of the butter. Bake Believe makes a dairy free chocolate chip!

Can I make them ahead and freeze?
Sure can! Once cooled, freeze in an airtight container for up to 3 months. Reheat in the microwave or oven.

Are these muffins kid-friendly?
Totally. The mini size is perfect for little hands and lunchboxes.

How many mini muffins does this make? This should make 24-32 depending on the size of your mini muffin pan. Fill them so they are just about full, but not quite!

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Greek Yogurt Mini Chocolate Chip Muffins

Yield: 24-32 mini muffins

Prep Time: 5 minutes

Cook Time: 10 minutes

Additional Time: 2 minutes

Total Time: 2 minutes

These Greek yogurt mini muffins with chocolate chips are soft, moist, and easy to make with simple ingredients. Made with Greek yogurt for added protein and tenderness, they’re perfect for breakfast, snacks, lunchboxes, or meal prep.

Print

Ingredients

• 1 cup flour
• 1 cup plain Greek yogurt
• 1/3 cup honey or maple syrup
• 1/4 cup unsalted butter, melted and slightly cooled
• 2 eggs, lightly beaten
• 2 teaspoons pure vanilla extract
• 1 teaspoon baking powder
• 1/2 teaspoon baking soda
• 1/4 teaspoon salt
• 3/4 cup chocolate chips- we like to use mini chocolate chips

Instructions

1. Preheat oven to 375 F and grease a 24-cup mini muffin pan (do not need to grease silicone).
2. Mix flour, baking powder, baking soda, and salt in a medium bowl.
3. Whisk yogurt, honey, eggs, butter, and vanilla in another bowl until smooth.
4. Fold wet ingredients into dry until just combined. A few streaks of flour are fine. You do NOT want to overmix these.
5. Stir in chocolate chips.
6. Fill the mini muffin pan so they are just about completely full, but not quite!. Bake 10-12 minutes until lightly golden and a tester comes out clean.
7. Cool in pan 2 minutes, then transfer to a wire rack.
   

Notes

Variations:

• Peanut Butter Chocolate Chip: Replace 1 egg with 1/4 cup peanut butter.
• Dye-Free Sprinkles
• Add dried fruit, nuts, or spices
• Stir in fresh fruit-for any juicier fruits you will want to subtract some liquid

Find more recipes like this at thegoodstuffbakeshop.com

Nutrition Information:

Yield: 28 Serving Size: 1
Amount Per Serving:Calories: 101Total Fat: 4gSaturated Fat: 2gUnsaturated Fat: 2gCholesterol: 19mgSodium: 79mgCarbohydrates: 14gFiber: 1gSugar: 6gProtein: 3g

Nutrition information is calculated automatically as a courtesy and is an estimate only. Accuracy is not guaranteed as values can vary based on specific brands and preparation methods used.

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