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Cinnamon Chip Chocolate Greek Yogurt Muffins

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Crazy moist, low on sugar, and rich in chocolate flavor, these cinnamon chip chocolate Greek yogurt muffins are just like your favorite bakery! This chocolate Greek yogurt muffin recipe is freezer friendly, and a perfect make-ahead breakfast for the family.

I remember my mom buying muffins when I was a kid. They were great (and HUGE, because she bought them at Costco or SAMS), but I didn’t fully understand why. Couldn’t we just make them at home in the morning if we wanted?

Now that I’m older, with a family, and approximately 15 different schedules for four people, I get it. And if someone could explain to me how there’s so much going on with so few people, I’d appreciate it. In the meantime, I’ll be baking muffins.

chocolate greek yogurt muffins in baking pan

Now darlings, if you’re like me, you’re a savory breakfast person. If I’m doing any kind of meal prep for breakfast, it’s usually a recipe like this zucchini herb bake or my low carb breakfast bake. But my little humans like the sweeter dishes, and they still think eating a muffin is akin to eating a cupcake. So muffins we make.

These chocolate Greek yogurt muffins are really good! In fact, the texture reminds me of those warehouse bakery chocolate muffins because it’s so moist! You can thank the Greek yogurt for the lovely crumb, and taking these from “definitely just eating dessert” to “passable for breakfast”. A little less fat than butter, and definitely more protein.

What kind of Greek yogurt should I use for baking muffins?

The Godmother “talking from experience” answer: use the kind you have on hand. My family doesn’t notice the difference and they’re picky because they’re spoiled.

The more “official baker book” answer: When using Greek yogurt in baking as a substitute for a fat, a full fat yogurt will give you the best results. This is because you don’t remove all the fat, just some of it.

close up of muffin to highlight the crumb and moist texture

But do you see how gorgeous the crumb is on these chocolate muffins? I use a plain nonfat Greek yogurt. 90% of the time, that’s what I use because it’s what I have in the house. In this recipe, there is no significant impact on the final product. In fact, you could probably even use a vanilla flavored Greek yogurt too with delicious results.

What happens if I substitute applesauce for the oil?

Here’s where you can change the texture, especially if you use nonfat yogurt and applesauce. At first, it won’t really be noticeable. BUT, the applesauce and nonfat yogurt muffins will dry out a little quicker than those made with more fat. So you’ll want to freeze any completely cool, but unconsumed muffins within 72 hours.

Do I have to use cinnamon chips?

No, of course not, my dears. You use what makes you happy. I used cinnamon chips because I spied a bag in my pantry, and we like the cinnamon and chocolate combination (see Mexican chocolate cake recipe here).

chocolate greek yogurt muffin on a black plate ready to serve in a white and aqua paper muffin liner

If you don’t like cinnamon or don’t have any chips on hand, use regular chocolate chips, white chocolate chips, even mint chips if you want mint chocolate muffins. There’s no hard and fast rule here regarding what baking chip you use. Muffins are not that serious.

cinnamon chip chocolate greek yogurt muffin close up on a black plate with cooling rack in the background

I hope you give this chocolate Greek yogurt muffin recipe a try and love it as much as we do. If you aren’t running to your kitchen immediately, don’t forget to pin it, share it, bookmark, print, whatever you need to do to keep this recipe easily accessible. Happy baking, darlings!

Cinnamon Chip Chocolate Greek Yogurt Muffins

Cinnamon Chip Chocolate Greek Yogurt Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes

Crazy moist, low on sugar, and rich in chocolate flavor, these cinnamon chip chocolate Greek yogurt muffins are just like your favorite bakery!


  • 1 cup all-purpose flour
  • 1/3 cup brown sugar, packed (see notes)
  • 1/3 cup unsweetened cocoa powder
  • 3/4 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 cup cinnamon chips (see notes)
  • 2 large eggs
  • 1/2 cup plain or vanilla Greek yogurt
  • 1/2 cup milk
  • 1/4 cup neutral-flavored oil or unsweetened applesauce
  • 1/2 teaspoon vanilla extract


  1. Preheat your oven to 325 F and prepare a 12-count muffin tin by either spraying with nonstick spray and dusting with flour, or lining with paper cupcake liners. Set aside.
  2. In a large mixing bowl, whisk together the first 6 ingredients. Yes, this includes the baking chips.
  3. In another, smaller bowl, mix together the eggs, yogurt, milk, oil, and vanilla.
  4. Add the wet ingredients to the dry ingredients in 2 batches. Stirring until just combined. Scrape the sides of the bowl as needed.
  5. Fill each cupcake well 2/3 full with batter. Bake the muffins for 15-18 minutes or until a tester inserted in a center muffin comes out with no more than a few moist crumbs attached. Be careful not to over bake.
  6. Allow the muffins to rest in the muffin tin 5 minutes before removing to cool completely on a cooling rack.
  7. Cooled muffins may be stored in an airtight container at room temperature up to 3 days or frozen up to 3 months. (See notes)


  • If you prefer a sweeter muffin, increase the sugar to 1/2 cup. Since we prefer our muffins on the less sweet side, 1/3 cup is fine.
  • Feel free to substitute another baking chip of your choice.
  • If in particularly humid climates where bread spoils quickly on the counter, I'd recommend storing muffins in the refrigerator instead of on the counter. To thaw frozen muffins, microwave 15-20 seconds.

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