My favorite 1-bowl Greek Yogurt muffins that taste like they came straight from a bakery! Made with almond and oat flour and sweetened with maple syrup, they bake up super tender and fluffy with over 6.5g protein each. They're naturally gluten free, super easy to make, and wholesome enough for breakfast. An immediate hit with my kids!

When my friend took a bite of these, the first thing she texted me was "these are bakery level!" After thanking her for the ego boost, I thought...hallelujah!
That's EXACTLY what I was going for. It's wild how almond flour gives that plush, cake-like texture you usually only get from white flour.
So many healthier muffins are dense or dry but protein-packed Greek yogurt, our hero here, keeps them extra moist and far more satisfying than your average sugar bomb chocolate chip muffin. The dietitian in me is so proud!!
They're perfectly sweet, tender, chocolately, and filling enough that I feel excellent about serving them at snack time.
These ingredient details changed the game
- The key to getting perfect texture every time is using oat flour (which is more dry) in addition to high-fat almond flour. It was clear in testing the almond flour alone doesn't yield that "classic" crumb. The oat flour helps keep them light and fluffy!
- A splash of almond extract makes the flavor absolutely next level. You only need a tiny amount, but trust me, don't skip it!
- I thought I'd need more oil here but the Greek yogurt adds plenty of moisture, limiting the need for added fat. In testing I actually prefered the flavor of olive oil to butter! Who would've thunk it?
Let's make them!






If you bake in a metal muffin tin (I tested both!), they'll look more domed like this:

Gentler heat is where these shine
I also tried baking these starting at 425°F for seven minutes then lowering the heat to 350°F to create a more domed top. While that trick often works for traditional muffins, the almond flour caused the outsides to brown too quickly.
I learned my lesson that baking them at a steady lower temperature produced a more even rise, softer crumb and overall better texture.

Let me know if you make these beauts by leaving a comment and star rating below! I appreciate it TONS.
Print
Healthy Chocolate Chip Greek Yogurt Muffins
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Yield: 12 muffins 1x
- Category: Muffins
- Method: Baking
- Cuisine: American
- Diet: Gluten-Free
Description
My favorite 1-bowl Greek Yogurt muffins that taste like they came straight from a bakery! Made with almond and oat flour and sweetened with maple syrup, they bake up super tender and fluffy with over 6.5g protein each. They're naturally gluten free, super easy to make, and wholesome enough for breakfast. An immediate hit with my kids!
Note these are not overly sweet muffins. You can sprinkle tops with coarse sugar like turbinado or a packet of Sugar in the Raw for more sweetness. I like them even better on day two!
Ingredients
- ¾ cup plain Greek yogurt
- 2 large eggs
- ½ cup pure maple syrup
- 2 tbsp extra virgin olive oil
- 2 tsp pure vanilla extract
- ¼ tsp almond extract
- 1 ¼ cups packed almond flour (163g)
- 1 ¼ cups oat flour (124g)
- 1 tsp baking powder
- ½ tsp baking sida
- ¼ tsp fine sea salt
- ½ cup + 2 tbsp semi-sweet or dark chocolate chips, divided
Instructions
- Preheat oven to 350F. Spray a muffin tin well with oil spray or line with paper liners--they'll stick if you don't! (I use a silicone muffin tin.)
- Place yogurt, eggs, maple syrup, olive oil, vanilla and almond extract in a large mixing bowl. Whisk until completely smooth.
- Add almond flour (make sure it's packed in there!), oat flour (spooned and leveled), baking powder, baking soda, and salt. Use a whisk or rubber spatula to mix until almost combined. Don't over-mix. It will be thick, don't worry! Fold in ½ cup chocolate chips.
- Divide batter evenly into muffin tin (I use a handy muffin scoop). Top with remaining chocolate chips.
- Bake for 20-22 minutes, or until a toothpick comes out clean. The tops will be golden since almond flour browns more easily. Cool on a wire rack and enjoy warm, ideally with flaky salt! Store covered on the counter for up to 2 days then refrigerate.
Notes
Adapted from my raspberry Greek yogurt muffins




Kori Daniel says
These are utterly phenomenal!!!
Alexis Joseph, MS, RD says
YAYYY you made my day, Kori!! XOXO
Peggy says
Sounds delic! Can this be made in a loaf pan
Thank you
Alexis Joseph, MS, RD says
I haven't tested it, they don't always translate the same! I do have lots of loaf recipes I've tested though if you want to try one of those 🙂
Peggy says
Ok thank you! Your recipes are always good
Thanknyou for your quick response!!
Alexis Joseph, MS, RD says
You're so kind, thanks Peggy!
Pippy says
Absolutely awesome recipe.
It really turns out just as described.
Love the mix of the oats and the almond flour.
These muffins are so light.
I bake in my air fryer at 135 for 15 mins.
The batch worked out better than the first batch.
Will definitely be part of my regular baking recipes.
Thank you so much for sharing.
Will keep my eyes open for low or no added sugar and low or healthy fat options.
Alexis Joseph, MS, RD says
Ohhh air fryer, how cool! I haven't tried making muffins in there. I'm thrilled you loved, thank you Pippy! These sweet potato muffins, chocolate banana date muffins and oatmeal raisin cookies have no added sugar 🙂
Val says
I don't even know how to begin to describe how delicious these muffins are...! They taste like they're straight from a bakery but then because they're made with Greek yogurt, almond, and oat flours they're a bit lighter feeling which is just the perfect combo! These are so good that I'd even consider opting for one of these muffins over a chocolate chip cookie!
Alexis Joseph, MS, RD says
YESSS you get me, Val! Ahh thank you so much for this rave review. Totally agree about them being a bit lighter. Such a joy to share them with you XOXO