Mocha Chocolate Chunk Muffins

5 from 1 vote

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Moist and tender coffee flavored muffins filled with gooey chunks of chocolate. No oil, no butter, but so many mouthwatering flavors!

A mocha chocolate chunk muffin on a piece of parchment paper.

I am seriously stuck on coffee these days (see recent how to make cold brew coffee, homemade French vanilla coffee creamer, and cappuccino cookies). Seriously. It is one of my favorite things in the world and it’s one of my favorite flavors to put into baked goods. 

I’ve chatted before about how I love coffee in my chocolate, but I don’t love chocolate in my coffee. This homemade peppermint mocha creamer is that exception, and now these muffins have completely flipped my chocolate-in-coffee world upside down. Flip with me, won’t you?

A stack of mocha chocolate chunk. muffins.

I made some skinny muffins a few months ago and used the muffin batter for that recipe as a base for these mocha muffins, but thanks to a hefty dose of some chocolate chunks, their “skinny” factor is not really there. Sorrynotsorry.

There’s still no butter or oil in these muffins, so if you reduce the amount of chocolate chunks, you’ll mayyyyybe be able to call these “skinny-ish.” (technical term)

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All adjectives aside, let’s focus on the important part: the coffee flavor. For my chocolate layer cake, I use brewed coffee. For these mocha muffins, I didn’t want to add any extra moisture, but I still wanted strong coffee presence, so I settled on instant coffee granules.

A container of instant coffee granules.

I use these in my cappuccino cookies, and I also use them in a recipe in my new cookbook (ohmygosh, one of my favorites in the book). This is not the same as ground coffee. Instant coffee granules are formulated a bit differently so that they can easily be dissolved in water (to make instant coffee– duh).

They work perfectly for this muffin batter because you dissolve them into your wet ingredients.

You can also use espresso powder. Coffee flavor without too much moisture: SCORE!

Coffee grounds in a measuring cup.

The muffin recipe itself is pretty standard. No weird ingredients, but you may have to take a special trip to the grocery store if you don’t keep yogurt or unsweetened applesauce on hand. These two ingredients alone bring so much moisture to these muffins, you won’t even miss the butter or oil that aren’t part of the ingredient list.

An egg helps bind everything together to create a moist yet tender crumb inside each coffee-laden bite of dessert-for-breakfast goodness. I use granulated sugar and just a touch of brown sugar as the sweeteners. The brown sugar gives a little extra “oomph” and adds some caramel notes.

The most important part about mixing up these muffins is to be sure you don’t over mix the batter. Over mixing batter develops the gluten in the flour too much, resulting in a tough crumb. We want to keep the crumb nice and soft, so easy does it when you add your wet ingredients to your dry ones and then again when folding in the chocolate chunks.

Mocha chocolate chunk muffins on a plate.

For good measure, I like to stick a couple extra chocolate chunks into the tops of each muffin before they go into the oven. This ensures each one has a little something special gracing its top, making sure these muffins say “I’m deliciously coffee-y and chocolate-y all at one time.”

Do your baked goods talk to you? No? Just me. My life is weird.

Whip these muffins up for a sweet treat at breakfast, a nice addition to your brunch spread, or use them entirely as a dessert. They’re basically a cupcake without icing, so you can totally call them dessert.

So much coffee flavor with ooey gooey chocolate chunks melted into every single bite… These muffins will knock your socks off with their taste and texture and you’d never guess they are made with yogurt and applesauce.

Mocha chocolate chunk muffin sliced open to see the inside.

The only way to make these muffins better is to enjoy them with a nice steamy cup of coffee. I like my coffee with a side of coffee, thankyouverymuch. Coffee for the win.

Lots of coffee recipes around these parts. Check out these coffee recipes next: cappuccino cookies, how to cold brew coffee, coffee rolls, tiramisu brownies, and mocha cake.

Mocha Chocolate Chunk Muffins: Moist and tender coffee flavored muffins filled with gooey chunks of chocolate. No oil, no butter, but so many mouthwatering flavors!
5 from 1 vote
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Mocha Chocolate Chunk Muffins

Moist and tender coffee flavored muffins filled with gooey chunks of chocolate. No oil, no butter, but so many mouthwatering flavors!
Prep Time10 minutes
Bake Time18 minutes
Total Time28 minutes
Recipe Author Lynn April
Servings: 10 muffins


  • 1 and 1/2 cups whole wheat flour you may also use all-purpose or a combination of both; be sure to measure properly
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • ½ cup granulated sugar
  • 1/4 cup light brown sugar loosely packed
  • 1/2 cup unsweetened applesauce
  • 3/4 cup plain Greek yogurt or vanilla
  • 1/3 cup instant coffee granules or espresso powder not coffee grounds
  • 1 teaspoon vanilla extract
  • 1 large egg
  • 2/3 cup semi-sweet chocolate chunks reduce to ⅓ cup if you prefer a less sweet muffin


  • Preheat oven to 350ºF degrees. Spray a cupcake/muffin pan generously with nonstick cooking spray. Do not use liners. Set aside.
  • In a large bowl, toss together the flour, baking powder, baking soda, and salt. Set aside. In a separate medium bowl, whisk together both sugars, unsweetened applesauce, Greek yogurt, instant coffee granules and vanilla extract until smooth. Whisk in the egg until fully incorporated. Add the wet ingredients to the dry ingredients until just combined– do not over mix batter. Fold in the chocolate chunks.
  • Divide the batter evenly between 10 muffin cups (using an ice cream scoop with a trigger makes this easier). Stick a few extra chocolate chunks in the tops of the batter for aesthetics, if desired. Bake for 15-18 minutes or until a toothpick inserted in the middle comes out clean. Allow muffins to cool in pan 5-10 minutes before transferring to wire rack to cool completely. Muffins will stay fresh in an airtight container at room temperature up to one week. Muffins freeze well, up to 2 months. Thaw in microwave for 45-60 seconds before eating.
Did you make this recipe?Mention @freshaprilflours on Instagram or tag #freshaprilflours!

Nutrition Disclosure

All nutritional values are approximate and provided to the reader as a courtesy. Changing ingredients and/or quantities will alter the estimated nutritional calculations.

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  1. Ooh I can’t wait until we can sit down (or walk around) and share a coffee in real time! In the meantime I will have to bake up a big batch of these muffins (we are equal opportunity chocolate and coffee baked goods lovers here) and plan the trip 🙂
    I love that these are skinny-ish which means they are a totally legitimate weekend breakfast (um, yes dessert for breakfast) or pre-gym snack at work 🙂
    Pinning and winning with this recipe 🙂

    1. I’m sure it could, but I am unsure of baking time. I would start with about 22-24 minutes and test for doneness from there. Let me know how you make out!

  2. Can the unsweetened applesauce be optional? Or if there’s anything esle could be used to substitute it?

    1. Hi Esther– using the unsweetened applesauce is what keeps these muffins on the healthier side. You could most certainly use butter and/or oil, but that would change the recipe completely and I’m not exactly sure what those substitutions would be.

  3. Just baked. Not sure what I did wrong, I didn’t change anything in the recipe but the texture is rubbery. Sorry, didn’t like this.

    1. Bummer! I have not had these turn out rubbery, so I’m unsure of what happened, too. The only thing I could think of is if you used a fat free yogurt, which would make it so there was just about no fat in the muffins which could lead to a not-so-great texture.

  4. I’d like to try making these as donuts. I may add a bit more sugar in the form of honey and simply bake them. I’ll update if/when this is accomplished.

  5. 5 stars
    I made these muffins today and they are absolutely delicious. They are soft and moist. I used 1/2 ww flour and 1/2 of the recipe as white flour, also cut the white sugar in half though as I don’t like my baking too sweet and used dark chocolate chunks. Super yummy. Thanks for an awesome recipe