These Healthy Greek Yogurt Chocolate Chip Cookies with Melty Centers are soft, chewy, and utterly satisfying—all while being made with wholesome ingredients. They’re the perfect blend of indulgence and nutrition, making them ideal for a guilt-free treat any day of the week.

I first made these on a whim when craving something sweet but didn’t want the heaviness of traditional cookies. The Greek yogurt keeps them moist, the oat flour gives a tender texture, and the melty chocolate chips take them over the top. They’re great for after-school snacks, quick breakfast bites, or late-night cravings.

Plus, they’re a great introduction to healthy baking. If you’ve ever thought healthy meant sacrificing flavor, these cookies will absolutely change your mind. They’re easy enough for beginner bakers and delicious enough to impress even the most skeptical cookie fan. Whether you’re serving these at a casual family gathering or stashing a few for yourself, they’ll disappear fast!

Why You’ll Love These Cookies

Healthier alternative – Made with Greek yogurt, honey/maple syrup, and oat flour.
Simple ingredients – Only 8 wholesome pantry staples.
Soft, chewy texture – Thanks to yogurt and oat flour.
Perfect for kids and adults – Naturally sweetened and chocolatey.
Quick to make – Ready in under 30 minutes.
Customizable – Add nuts, dried fruit, or a sprinkle of sea salt.
Protein-packed – Thanks to Greek yogurt and egg.
Great for meal prep – Make a batch and enjoy all week.

Ingredients You’ll Need

½ cup Greek yogurt – Plain, full-fat or 2% for best texture and richness.
⅓ cup honey or maple syrup – Natural sweeteners with a touch of depth.
1 egg – Binds the cookies and gives them structure.
1 teaspoon vanilla extract – Enhances overall flavor.
1 cup oat flour – Soft and mild; make your own by blending rolled oats.
¼ cup mini chocolate chips – Every bite gets a hit of sweetness.
½ teaspoon baking powder – Lends lightness to the cookies.
Pinch of salt – Balances the flavors and boosts sweetness.

Step-by-Step Instructions

Preheat oven:
- Preheat to 350°F (175°C). Line a baking sheet with parchment paper or a silicone baking mat.
Mix wet ingredients:
- In a medium bowl, whisk together Greek yogurt, honey or maple syrup, egg, and vanilla until smooth.
Add dry ingredients:
- Stir in the oat flour, baking powder, and salt until a smooth dough forms. Avoid overmixing.
Fold in chocolate chips:
- Gently stir in the mini chocolate chips, making sure they’re evenly distributed throughout the dough.
Scoop and shape:
- Use a small cookie scoop or spoon to portion dough onto the baking sheet, spacing about 2 inches apart. Flatten slightly for even baking.
Bake:
- Bake for 10–12 minutes, until the edges are set and the tops are just slightly golden. Centers may appear soft—that’s what makes them gooey!
Cool and enjoy:
- Allow cookies to cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.

Serving and Storage Tips

Serve warm for gooey, melty centers and maximum flavor.
Pair with milk, coffee, or tea for a cozy snack or dessert.
Storage: Keep in an airtight container at room temperature for up to 3 days.
Refrigerate: Store in the fridge for up to 1 week.
Freeze: Freeze baked cookies in a sealed bag or container for up to 2 months. Reheat in the microwave for 10–15 seconds.
Portable snack: Great for lunchboxes or on-the-go fuel.

Helpful Notes

Chill the dough for 10–20 minutes if it's too sticky to handle or to enhance shape during baking.
Add-ins: Try chopped walnuts, pecans, dried cherries, raisins, or coconut flakes.
Texture tweaks: Want them chewier? Add 1 tablespoon nut butter to the dough.
Gluten-free: Use certified gluten-free oats for oat flour.
Dairy-free: Sub in plant-based yogurt and dairy-free chocolate chips.
Make it mini: Use a teaspoon-sized scoop for bite-sized treats.

Frequently Asked Questions

Can I use regular flour instead of oat flour?
Yes, but it will change the texture—start with ¾ cup and adjust to reach dough consistency.
Is Greek yogurt necessary?
It provides protein and moisture. You can sub in a thick, plain dairy-free yogurt if needed.
Can I double the recipe?
Absolutely! The dough doubles well, and baked cookies freeze beautifully.
Why are the centers soft?
That’s part of their magic! Slightly underbaked centers create a molten, lava-like effect.
Can I make them egg-free?
Yes—substitute with a flax egg (1 tablespoon flaxseed meal + 3 tablespoon water, rested for 5 mins). Texture will vary slightly.
Can I use flavored yogurt?
Plain is best, but vanilla Greek yogurt can work too—just reduce added sweetener slightly.

Final Thoughts

These Healthy Greek Yogurt Chocolate Chip Cookies with Melty Centers prove that wholesome and indulgent can go hand in hand. They come together quickly, satisfy your sweet tooth, and leave you feeling good—not sluggish. Whether you’re baking with kids, prepping snacks for the week, or simply craving a warm cookie, this recipe delivers.

Get creative with your mix-ins and make the recipe your own. Share them with family, friends, or enjoy them solo with a cozy drink. Either way, one batch likely won’t be enough!

Let me know how yours turn out, and drop your favorite healthy baking hacks or flavor combos in the comments below. Happy baking!

Healthy Greek Yogurt Chocolate Chip Cookies with Melty Centers

Emily

These soft and chewy cookies are naturally sweetened and made with Greek yogurt and oat flour for a healthier twist. With gooey chocolate chip centers and simple pantry ingredients, they’re perfect for everyday snacking, meal prep, or guilt-free indulgence.

Print Recipe Pin Recipe

Prep Time 10

Cook Time 12

Servings 12 cookies

Calories 120 kcal

Ingredients

½ cup Greek yogurt plain, full-fat or 2%
⅓ cup honey or maple syrup
1 egg
1 teaspoon vanilla extract
1 cup oat flour
¼ cup mini chocolate chips
½ teaspoon baking powder
Pinch of salt

Optional Add-ins:

Chopped walnuts pecans, or almonds
Dried cherries or raisins
1 tablespoon nut butter for extra chewiness
Coconut flakes or sea salt sprinkle

Instructions

Preheat oven to 350°F (175°C). Line a baking sheet with parchment paper.
In a bowl, whisk together Greek yogurt, honey/maple syrup, egg, and vanilla.
Add oat flour, baking powder, and salt. Stir until just combined.
Fold in mini chocolate chips. Chill dough 10–20 mins if too soft.
Scoop dough onto baking sheet and flatten slightly.
Bake for 10–12 minutes, until edges are set and centers are soft.
Cool on the pan for 5 minutes, then transfer to a wire rack. Enjoy warm!

Notes

Use certified gluten-free oats if needed.
Store in an airtight container for 3 days or refrigerate for 1 week.
Freeze baked cookies up to 2 months.
Reheat in the microwave for a melty center.