Soft, fluffy, and full of chocolatey flavor, these muffins will have you reaching for seconds (and thirds!). Greek yogurt adds extra protein and helps keep these moist for several days, making these a perfect start to your day.

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I am so excited for these muffins! I have been trying for a while to convert my blueberry muffins into chocolate, and I finally did it!

First, I decided to use greek yogurt instead of applesauce, to keep these from crumbling and also ensure a more consistent moisture balance. Applesauce can sometimes be too liquidy, meaning you need more flour, which in turn can make the muffin (or bread) dry out faster. Greek yogurt brings that moisture without requiring extra flour or cocoa.

Second, the obvious change I made was adding cocoa powder. However, you can’t just sub some cocoa for flour—you need slightly more of it than the amount of flour you removed (if that makes sense?). So I looked at a variety of similar recipes as well as my own experiences subbing out some flour for cocoa and settled on this ratio.

Wow. Talk about lovely cocoa flavor. It is rich without being too dark. And it’s not dry at all.

Add in chocolate chips and you have a delicious, easy, kid-approved muffin that you can even feel a little good about eating for breakfast—because Greek yogurt!

Why this recipe works

One key part of this recipe is the combination of butter and oil. It stays moist because of the oil, but using half butter helps it stay fluffy, too. It ends up being a lighter, fluffier muffin that’s still super moist and flavorful. Another key to the moisture is the Greek yogurt. It’s the perfect thickness to add some protein and structure but still keep the muffins moist for several days.

Finally, the chocolate flavor. I experimented with how much cocoa to add. You can’t simply substitute cocoa for flour, so I had to try a few ratios to get it exact. This ratio is just enough to give a rich chocolate flavor without being overly bitter or super dark (nothing against super dark muffins, I just know my daughter won’t eat them). Plus, the chocolate chips. I mean, you can’t have double chocolate without lots of chocolate chips. They add flavor and texture to these muffins, and are probably my favorite part.

Key ingredients

Plain Greek yogurt. This helps keep the bread so, so moist for days. Be sure it’s authentic Greek yogurt and doesn’t have thickeners in the ingredients. Also, use un-flavored, unsweetened, whole milk Greek yogurt.

Flour. Be sure to sift it and to measure carefully—spoon the flour into the measuring cup then level it off with the flat side of a knife (known as spoon-then-level).

Cocoa powder. Use plain cocoa, not sweetened. For this recipe it doesn’t matter if it’s Dutch processes or not.

Salt. Try to use sea salt, if possible, as it won’t create an overly salted taste and is actually better for you!

Baking powder. Not baking soda! Baking powder is more delicate and helps this rise without being dense.

Eggs. Be sure these are room temperature so they mix well with the other ingredients! If you forget to take them out ahead of time, you can put them in a bowl of warm (not hot) water for 15 minutes.

Oil. I suggest avocado or grape seed oil, as these have a mild flavor but are healthier than vegetable or canola.

Vanilla. Use pure! Imitation will have a slightly different flavor and won’t give you the same pleasant flavor.

Butter. I suggest European style, as it has less water. Be sure to use unsalted, or omit the salt in the recipe. Be sure to melt it without letting it boil, as we don’t want browned butter.

Brown and granulated sugar. Brown sugar helps this stay moist while granulated helped it rise. Using both gives you the best of both worlds.

Chocolate chips. You can use any kind you like. I used semi-sweet, but dark or milk chocolate would do, too.

How to make double chocolate greek yogurt muffins

1. Melt your butter. Set aside to cool while you mix everything else.

2. Sift and whisk together the dry ingredients.

3. Whisk wet ingredients. Start with the Greek yogurt, oil, vanilla, and egg and whisk well. Stream in the butter, whisking quickly.

4. Whisk in the sugars for 1 minute. This helps them dissolve somewhat before baking.

5. Fold in the dry ingredients. Don’t mix fully—leave some flour streaks to be folded in during the next step.

6. Fold in chocolate chips. This step will mix in all flour, but don’t worry if you see some flour lumps—just make sure there’s not visible flour.

7. Bake for 18-23 minutes. Check early to make sure it doesn’t over bake. If it starts to darken too early, tent loosely with foil.

Enjoy!

Tips and FAQ’s for this recipe

Can I sub the Greek yogurt?

Yes! You can use the same amount of mashed bananas (about 2 medium bananas) or pumpkin puree. You can also sub applesauce but will need to add about 2 tablespoons flour to the recipe.

How do I know it’s baked through?

I always use a toothpick, but a small knife or kebab skewer will work, too. You want to catch the muffins when they just barely stop being raw, as they will cook a little more in the pan while they cool. The top will not change color as much as other muffins, since the chocolate is already dark. So try to use a toothpick to check for moist crumbs but no raw batter.

Do I have to sift the flour and cocoa?

Yes! Sifting is key in baking, particularly in anything cake-y. It helps it mix into the wet ingredients more easily, preventing clumps as well as circumventing the urge to over-stir and create a tough, rubbery texture. In this recipe especially, sifting is needed because cocoa powder tends to be very clumpy and cannot mix properly if not sifted.

Spoon then level your flour

Don’t scoop your flour! I never knew this until I started blogging, but it seriously makes a big difference. You will end up with roughly 25% more flour than the recipe called for if you just doonk (official baking term right there) your measuring spoon into the flour container and scoop. Gently spoon your flour into your measuring cup then level it off with the back of a knife. Trust me! It makes a difference.

My muffin tools

Here are my must-have tools I use for making these muffins. Affiliate links provided.

Whisk (or stand mixer or handheld mixer)

Mesh sieve (because sifting is KEY )

Cupcake/muffin pans (I’ve used many over the years and these are the most consistently successful.)

Increasing or decreasing the recipe

I wrote this recipe to make about 14-16 muffins, but you can easily decrease it for about 8 muffins or increase it to get 24 muffins. Below are the measurements for a reduced or increased batch.

To make 8 muffins (a half batch):

½ cup plus 2 tablespoons (85g) all-purpose flour, spooned and leveled
¼ cup (22g) cocoa powder, sifted

1 teaspoon (4g) baking powder
¼ teaspoon (1g) salt
½ cup (113g) plain, whole milk Greek yogurt, room temperature
½ tablespoon (7g) pure vanilla extract
1 large egg, room temperature
2 tablespoons (28g) avocado or vegetable oil
2 tablespoons (28g) melted butter
¼ cup (50g) granulated sugar
¼ cup (50g) packed brown sugar (light or dark will work)
½ cup (85g) chocolate chips

To make 24 muffins (a triple batch):

1 ¾ cups plus 2 tablespoons (255g) all-purpose flour, spooned then leveled
¾ cup (64g) cocoa powder, sifted

3 teaspoons (12g) baking powder
¾ teaspoon (4g) salt
1 ½ cup (about 340g) plain, whole milk Greek yogurt, room temperature
1 ½ tablespoons (19g) pure vanilla extract
3 large eggs, room temperature
6 tablespoons (84g) avocado or vegetable oil
6 tablespoons (84g) melted butter
¾ cup (150g) granulated sugar
¾ cup (150g) brown sugar
1 ½ cups (255g) chocolate chips

You might also like:

Chocolate Chip Banana Bread

Blueberry Streusel Muffins

Pumpkin Donuts

Pumpkin Streusel Muffins

Double Crumb Greek Yogurt Coffee Cake

Double Chocolate Greek Yogurt Muffins

Print recipe

prep time: 5-10 minutes
bake time: 18-23 minutes
total time: 33 minutes

servings: 14-16 muffins (see note* above for 8 or 24 muffins)

Ingredients:

1 ¼ cups (170g) all-purpose flour, spooned and leveled
½ cup (48g) cocoa powder
2 teaspoons (8g) baking powder
½ teaspoon (4g) salt
1 cup (227g) whole milk, plain Greek yogurt, room temperature
1 tablespoon (13g) pure vanilla extract
2 large eggs, room temperature
4 tablespoons (56g) avocado or vegetable oil
4 tablespoons (56g) melted butter
½ cup (100g) granulated sugar
½ cup (100g) packed brown sugar (light or dark will work)
1 cup (170g) chocolate chips (or to taste)

Instructions:

Preheat your oven to 350F/175C. Line a muffin/cupcake pan with muffin liners (or grease it with butter and flour or baking spray).
Melt the butter and set aside. Don’t let it cool enough to solidify, but do let it cool somewhat before using.
Using a large fine mesh sieve, sift then whisk together the flour, cocoa powder, baking powder, and salt. You can also add a dash of cinnamon if you’d like. Set aside.
In a medium to large mixing bowl, whisk the Greek yogurt, vanilla, eggs, and oil until well blended. Slowly pour in the butter while whisking quickly.
Add the sugar and brown sugar to the wet ingredients and whisk for about 1 minute. You can whisk it by hand or, if using a stand or hand mixer, mix on medium.
Fold in the flour mixture gently until mostly combined, with some visibly dry flour in spots. Fold in the chocolate chips until well-distributed. This step will cause the rest of the flour to mix in, but it should still have some lumps in it.
Divide between your prepared muffin liners/pan. Top with some more chocolate chips.
Bake for 18-23 minutes, until matte on top and a toothpick inserted in a middle muffin comes out with some moist crumbs. Check early so it doesn’t over bake. Let muffins cool in pan 5-10 minutes. Remove and let either serve immediately or let cool completely before storing in an airtight container.

Enjoy with your morning coffee!

Store leftovers in an airtight container.